X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSurfacingUtil.java;h=73544b7f96b42024ad4ae955e70d9b5b1d1496c1;hb=c914fef4ec7f50e4cf01375a30207992c84659a3;hp=1cc2c7a0c4da0718edc106d48c4219ba93dbb410;hpb=cec76926e7d634373e238e61b805c723ef4c0ca7;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index 1cc2c7a..73544b7 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -22,10 +22,11 @@
 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
 //
 // Contact: phylosoft @ gmail . com
-// WWW: www.phylosoft.org/forester
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
 
 package org.forester.surfacing;
 
+import java.awt.Color;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
@@ -39,6 +40,7 @@ import java.util.Collections;
 import java.util.Comparator;
 import java.util.HashMap;
 import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Map.Entry;
@@ -65,57 +67,60 @@ import org.forester.go.GoNameSpace;
 import org.forester.go.GoTerm;
 import org.forester.go.PfamToGoMapping;
 import org.forester.io.parsers.nexus.NexusConstants;
+import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
+import org.forester.io.parsers.util.ParserUtils;
 import org.forester.io.writers.PhylogenyWriter;
-import org.forester.msa.MsaCompactor.SORT_BY;
 import org.forester.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
 import org.forester.phylogeny.PhylogenyNode;
-import org.forester.phylogeny.PhylogenyNodeI.NH_CONVERSION_SUPPORT_VALUE_STYLE;
+import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
 import org.forester.phylogeny.data.BinaryCharacters;
 import org.forester.phylogeny.data.Confidence;
+import org.forester.phylogeny.data.Taxonomy;
+import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
 import org.forester.protein.BasicDomain;
 import org.forester.protein.BasicProtein;
 import org.forester.protein.BinaryDomainCombination;
 import org.forester.protein.Domain;
-import org.forester.protein.DomainId;
 import org.forester.protein.Protein;
 import org.forester.species.Species;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
-import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
 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;
 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 {
 
-    private final static NumberFormat       FORMATTER                        = new DecimalFormat( "0.0E0" );
-    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}$" );
-    private static final boolean            USE_LAST                         = true;
+    public final static Pattern              PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
+    private final static Map<String, String> _TAXCODE_HEXCOLORSTRING_MAP      = new HashMap<String, String>();
+    private 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 );
+                                                                                      }
+                                                                                  }
+                                                                              };
+    private final static NumberFormat        FORMATTER_3                      = new DecimalFormat( "0.000" );
 
     private SurfacingUtil() {
         // Hidden constructor.
@@ -123,49 +128,20 @@ public final class SurfacingUtil {
 
     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
-        final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
-        for( final DomainId domain_id : all_cd.keySet() ) {
+        final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
+        for( final String domain_id : all_cd.keySet() ) {
             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
         }
     }
 
     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
-                                             final SortedSet<DomainId> domain_ids ) {
-        final SortedSet<DomainId> domains = genome.getAllDomainIds();
-        for( final DomainId domain : domains ) {
+                                             final SortedSet<String> domain_ids ) {
+        final SortedSet<String> domains = genome.getAllDomainIds();
+        for( final String domain : domains ) {
             domain_ids.add( domain );
         }
     }
 
-    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( "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 DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
         for( final DomainSimilarity similarity : similarities ) {
@@ -174,508 +150,372 @@ 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 );
+    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 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 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 {
-                        dc_gain_counts.put( dc, 1 );
+                        all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
+                                .getCharacter( c ) ) );
                     }
                 }
             }
-            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>();
-            final DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
-            final DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
-            final 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() );
+        }
+    }
+
+    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 );
+        }
+        else {
+            parameters_sb.append( ", Cutoff-scores-file: not-set" );
+        }
+        if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
+            parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
+        }
+        else {
+            parameters_sb.append( ", Max-overlap: not-set" );
+        }
+        if ( no_engulfing_overlaps ) {
+            parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
+        }
+        else {
+            parameters_sb.append( ", Engulfing-overlaps: allowed" );
+        }
+        if ( ignore_dufs ) {
+            parameters_sb.append( ", Ignore-dufs: true" );
+        }
+        else {
+            parameters_sb.append( ", Ignore-dufs: false" );
+        }
+        parameters_sb.append( ", DC type (if applicable): " + dc_type );
+        return parameters_sb;
+    }
+
+    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" ) ) );
+        split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_B.html" ) ) );
+        split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_C.html" ) ) );
+        split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_D.html" ) ) );
+        split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_E.html" ) ) );
+        split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_F.html" ) ) );
+        split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_G.html" ) ) );
+        split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_H.html" ) ) );
+        split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_I.html" ) ) );
+        split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_J.html" ) ) );
+        split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_K.html" ) ) );
+        split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_L.html" ) ) );
+        split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_M.html" ) ) );
+        split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_N.html" ) ) );
+        split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_O.html" ) ) );
+        split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_P.html" ) ) );
+        split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_Q.html" ) ) );
+        split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_R.html" ) ) );
+        split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_S.html" ) ) );
+        split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_T.html" ) ) );
+        split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_U.html" ) ) );
+        split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_V.html" ) ) );
+        split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_W.html" ) ) );
+        split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_X.html" ) ) );
+        split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_Y.html" ) ) );
+        split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_Z.html" ) ) );
+        split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
+                + "_domains_0.html" ) ) );
+    }
+
+    public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
+        final Map<String, Integer> m = new HashMap<String, Integer>();
+        for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
+            final PhylogenyNode n = iter.next();
+            if ( n.getNodeData().isHasTaxonomy() ) {
+                final Taxonomy t = n.getNodeData().getTaxonomy();
+                final String c = t.getTaxonomyCode();
+                if ( !ForesterUtil.isEmpty( c ) ) {
+                    if ( n.getNodeData().getTaxonomy() == null ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
                     }
-                    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() );
+                    final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
+                    if ( ForesterUtil.isEmpty( id ) ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
                     }
-                    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() );
+                    if ( m.containsKey( c ) ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
                     }
-                    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 int iid = Integer.valueOf( id );
+                    if ( m.containsValue( iid ) ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
+                    }
+                    m.put( c, iid );
                 }
-                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 );
+            }
+            else {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
+            }
+        }
+        return m;
+    }
+
+    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;
+                printable_domain_similarity.setDetailedness( detailedness );
+            }
+        }
+    }
+
+    public static void doit( final List<Protein> proteins,
+                             final List<String> query_domain_ids_nc_order,
+                             final Writer out,
+                             final String separator,
+                             final String limit_to_species,
+                             final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
+        for( final Protein protein : proteins ) {
+            if ( ForesterUtil.isEmpty( limit_to_species )
+                    || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
+                if ( protein.contains( query_domain_ids_nc_order, true ) ) {
+                    out.write( protein.getSpecies().getSpeciesId() );
+                    out.write( separator );
+                    out.write( protein.getProteinId().getId() );
+                    out.write( separator );
+                    out.write( "[" );
+                    final Set<String> visited_domain_ids = new HashSet<String>();
+                    boolean first = true;
+                    for( final Domain domain : protein.getProteinDomains() ) {
+                        if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
+                            visited_domain_ids.add( domain.getDomainId() );
+                            if ( first ) {
+                                first = false;
+                            }
+                            else {
+                                out.write( " " );
+                            }
+                            out.write( domain.getDomainId() );
+                            out.write( " {" );
+                            out.write( "" + domain.getTotalCount() );
+                            out.write( "}" );
                         }
                     }
-                    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 );
-                        }
+                    out.write( "]" );
+                    out.write( separator );
+                    if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
+                            .equals( SurfacingConstants.NONE ) ) ) {
+                        out.write( protein.getDescription() );
                     }
-                    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;
-                        }
+                    out.write( separator );
+                    if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
+                            .equals( SurfacingConstants.NONE ) ) ) {
+                        out.write( protein.getAccession() );
                     }
+                    out.write( SurfacingConstants.NL );
                 }
             }
-            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.flush();
+    }
+
+    public static void domainsPerProteinsStatistics( final String genome,
+                                                     final List<Protein> protein_list,
+                                                     final DescriptiveStatistics all_genomes_domains_per_potein_stats,
+                                                     final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
+                                                     final SortedSet<String> domains_which_are_always_single,
+                                                     final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
+                                                     final SortedSet<String> domains_which_never_single,
+                                                     final Writer writer ) {
+        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
+        for( final Protein protein : protein_list ) {
+            final int domains = protein.getNumberOfProteinDomains();
+            //System.out.println( domains );
+            stats.addValue( domains );
+            all_genomes_domains_per_potein_stats.addValue( domains );
+            if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
+                all_genomes_domains_per_potein_histo.put( domains, 1 );
             }
-            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 );
+            else {
+                all_genomes_domains_per_potein_histo.put( domains,
+                                                          1 + all_genomes_domains_per_potein_histo.get( domains ) );
+            }
+            if ( domains == 1 ) {
+                final String domain = protein.getProteinDomain( 0 ).getDomainId();
+                if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+                    if ( domains_which_never_single.contains( domain ) ) {
+                        domains_which_never_single.remove( domain );
+                        domains_which_are_sometimes_single_sometimes_not.add( domain );
+                    }
+                    else {
+                        domains_which_are_always_single.add( domain );
                     }
                 }
-                for( int i = 0; i < nodes.size() - 1; ++i ) {
-                    for( int j = i + 1; j < nodes.size(); ++j ) {
-                        final PhylogenyNode lca = PhylogenyMethods.obtainLCA( 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 if ( domains > 1 ) {
+                for( final Domain d : protein.getProteinDomains() ) {
+                    final String domain = d.getDomainId();
+                    // System.out.println( domain );
+                    if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
+                        if ( domains_which_are_always_single.contains( domain ) ) {
+                            domains_which_are_always_single.remove( domain );
+                            domains_which_are_sometimes_single_sometimes_not.add( domain );
                         }
                         else {
-                            lca_species = lca.getName();
+                            domains_which_never_single.add( domain );
                         }
-                        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" );
-                    }
+        }
+        try {
+            writer.write( genome );
+            writer.write( "\t" );
+            if ( stats.getN() >= 1 ) {
+                writer.write( stats.arithmeticMean() + "" );
+                writer.write( "\t" );
+                if ( stats.getN() >= 2 ) {
+                    writer.write( stats.sampleStandardDeviation() + "" );
                 }
-                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" );
-                    }
+                else {
+                    writer.write( "" );
                 }
-                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() );
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained once, domain counts:" );
-                w.write( "\n" );
-                w.write( gained_once_domain_count_stats.toString() );
-                w.write( "\n" );
-                w.write( "\n" );
-                w.write( "Gained multiple times, protein lengths:" );
-                w.write( "\n" );
-                w.write( gained_multiple_times_lengths_stats.toString() );
-                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();
+                writer.write( "\t" );
+                writer.write( stats.median() + "" );
+                writer.write( "\t" );
+                writer.write( stats.getN() + "" );
+                writer.write( "\t" );
+                writer.write( stats.getMin() + "" );
+                writer.write( "\t" );
+                writer.write( stats.getMax() + "" );
+            }
+            else {
+                writer.write( "\t" );
+                writer.write( "\t" );
+                writer.write( "\t" );
+                writer.write( "0" );
+                writer.write( "\t" );
+                writer.write( "\t" );
             }
+            writer.write( "\n" );
         }
         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 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 int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
-        int overlap_count = 0;
-        for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
-            if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
-                ++overlap_count;
-            }
-        }
-        return overlap_count;
-    }
-
-    public static void checkForOutputFileWriteability( final File outfile ) {
-        final String error = ForesterUtil.isWritableFile( outfile );
-        if ( !ForesterUtil.isEmpty( error ) ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME, error );
-        }
-    }
-
-    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 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<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
-        final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
-                .size() );
-        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<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
-            throws IOException {
-        final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, "\t" );
-        final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
-        for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
-            final DomainId domain_id = new DomainId( 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;
-    }
-
-    private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
-        final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
-        final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
-        for( final DomainId domain_id : cds.keySet() ) {
-            final CombinableDomains cd = cds.get( domain_id );
-            binary_combinations.addAll( cd.toBinaryDomainCombinations() );
-        }
-        return binary_combinations;
-    }
-
-    public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
-                                                            final Detailedness detailedness,
-                                                            final GoAnnotationOutput go_annotation_output,
-                                                            final Map<GoId, GoTerm> go_id_to_term_map,
-                                                            final GoNameSpace go_namespace_limit ) {
-        if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
-            throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
-        }
-        for( final DomainSimilarity domain_similarity : domain_similarities ) {
-            if ( domain_similarity instanceof PrintableDomainSimilarity ) {
-                final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
-                printable_domain_similarity.setDetailedness( detailedness );
-                printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
-                printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
-                printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
-            }
+            e.printStackTrace();
         }
     }
 
@@ -702,10 +542,6 @@ public final class SurfacingUtil {
                     out.write( species + "\t" );
                 }
                 out.write( ForesterUtil.LINE_SEPARATOR );
-                // DescriptiveStatistics stats_for_domain = domain_lengths
-                //         .calculateMeanBasedStatistics();
-                //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
-                //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
             }
         }
         out.write( ForesterUtil.LINE_SEPARATOR );
@@ -739,22 +575,97 @@ public final class SurfacingUtil {
             }
         }
         out.close();
-        //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
-        //        for( int i = 0; i < number_of_genomes; ++i ) {
-        //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
-        //            histogram_datas
-        //                    .add( new HistogramData( species.toString(), domain_lengths_table
-        //                            .calculateMeanBasedStatisticsForSpecies( species )
-        //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
-        //        }
-        //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
-        //        hf.setVisible( true );
         System.gc();
     }
 
     /**
+     * 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 
+     * @throws IOException
+     */
+    public static void executeFitchGainsAnalysis( final File output_file,
+                                                  final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
+                                                  final int sum_of_all_domains_encountered,
+                                                  final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
+                                                  final boolean is_gains_analysis ) throws IOException {
+        checkForOutputFileWriteability( output_file );
+        final Writer out = ForesterUtil.createBufferedWriter( output_file );
+        final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
+                .listToSortedCountsMap( all_bin_domain_combinations_changed );
+        final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
+        final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
+        int above_one = 0;
+        int one = 0;
+        for( final Object bdc_object : bdc_to_counts.keySet() ) {
+            final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
+            final int count = bdc_to_counts.get( bdc_object );
+            if ( count < 1 ) {
+                ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "count < 1 " );
+            }
+            out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
+            if ( count > 1 ) {
+                all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
+                all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
+                above_one++;
+            }
+            else if ( count == 1 ) {
+                all_domains_in_combination_changed_only_once.add( bdc.getId0() );
+                all_domains_in_combination_changed_only_once.add( bdc.getId1() );
+                one++;
+            }
+        }
+        final int all = all_bin_domain_combinations_encountered.size();
+        int never_lost = -1;
+        if ( !is_gains_analysis ) {
+            all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
+            never_lost = all_bin_domain_combinations_encountered.size();
+            for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
+                out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
+            }
+        }
+        if ( is_gains_analysis ) {
+            out.write( "Sum of all distinct domain combinations appearing once               : " + one
+                    + ForesterUtil.LINE_SEPARATOR );
+            out.write( "Sum of all distinct domain combinations appearing more than once     : " + above_one
+                    + 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: "
+                    + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
+        }
+        else {
+            out.write( "Sum of all distinct domain combinations never lost                   : " + never_lost
+                    + ForesterUtil.LINE_SEPARATOR );
+            out.write( "Sum of all distinct domain combinations lost once                    : " + one
+                    + ForesterUtil.LINE_SEPARATOR );
+            out.write( "Sum of all distinct domain combinations lost more than once          : " + above_one
+                    + 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 );
+        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_gained if null ignored, otherwise this is to list all binary domain combinations
      * which were gained under unweighted (Fitch) parsimony.
@@ -764,19 +675,22 @@ public final class SurfacingUtil {
                                                  final String outfile_name,
                                                  final DomainParsimonyCalculator domain_parsimony,
                                                  final Phylogeny phylogeny,
-                                                 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                                 final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                  final Map<GoId, GoTerm> go_id_to_term_map,
                                                  final GoNameSpace go_namespace_limit,
                                                  final String parameters_str,
-                                                 final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
-                                                 final SortedSet<DomainId> positive_filter,
+                                                 final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
+                                                 final SortedSet<String> positive_filter,
                                                  final boolean output_binary_domain_combinations_for_graphs,
                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
                                                  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 ) {
+                                                 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 String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
         final String date_time = ForesterUtil.getCurrentDateTime();
         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
@@ -784,7 +698,9 @@ public final class SurfacingUtil {
         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
-        writeToNexus( outfile_name, domain_parsimony, phylogeny );
+        if ( write_to_nexus ) {
+            writeToNexus( outfile_name, domain_parsimony, phylogeny );
+        }
         // DOLLO DOMAINS
         // -------------
         Phylogeny local_phylogeny_l = phylogeny.copy();
@@ -827,7 +743,8 @@ public final class SurfacingUtil {
                                        domain_id_to_secondary_features_maps,
                                        all_pfams_encountered,
                                        all_pfams_gained_as_domains,
-                                       "_dollo_gains_d" );
+                                       "_dollo_gains_d",
+                                       tax_code_to_id_map );
         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
                                        go_id_to_term_map,
                                        go_namespace_limit,
@@ -842,22 +759,24 @@ public final class SurfacingUtil {
                                        domain_id_to_secondary_features_maps,
                                        all_pfams_encountered,
                                        all_pfams_lost_as_domains,
-                                       "_dollo_losses_d" );
-        writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
-                                       go_id_to_term_map,
-                                       go_namespace_limit,
-                                       false,
-                                       domain_parsimony.getGainLossMatrix(),
-                                       null,
-                                       outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
-                                       sep,
-                                       ForesterUtil.LINE_SEPARATOR,
-                                       "Dollo Parsimony | Present | Domains",
-                                       "",
-                                       domain_id_to_secondary_features_maps,
-                                       all_pfams_encountered,
-                                       null,
-                                       "_dollo_present_d" );
+                                       "_dollo_losses_d",
+                                       tax_code_to_id_map );
+        //        writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
+        //                                       go_id_to_term_map,
+        //                                       go_namespace_limit,
+        //                                       false,
+        //                                       domain_parsimony.getGainLossMatrix(),
+        //                                       null,
+        //                                       outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
+        //                                       sep,
+        //                                       ForesterUtil.LINE_SEPARATOR,
+        //                                       "Dollo Parsimony | Present | Domains",
+        //                                       "",
+        //                                       domain_id_to_secondary_features_maps,
+        //                                       all_pfams_encountered,
+        //                                       null,
+        //                                       "_dollo_present_d",
+        //                                       tax_code_to_id_map );
         preparePhylogeny( local_phylogeny_l,
                           domain_parsimony,
                           date_time,
@@ -884,7 +803,7 @@ public final class SurfacingUtil {
                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
             }
             else {
-                domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
+                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 );
@@ -944,7 +863,8 @@ public final class SurfacingUtil {
                                            null,
                                            all_pfams_encountered,
                                            all_pfams_gained_as_dom_combinations,
-                                           "_fitch_gains_dc" );
+                                           "_fitch_gains_dc",
+                                           tax_code_to_id_map );
             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
                                            go_id_to_term_map,
                                            go_namespace_limit,
@@ -959,22 +879,24 @@ public final class SurfacingUtil {
                                            null,
                                            all_pfams_encountered,
                                            all_pfams_lost_as_dom_combinations,
-                                           "_fitch_losses_dc" );
-            writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
-                                           go_id_to_term_map,
-                                           go_namespace_limit,
-                                           true,
-                                           domain_parsimony.getGainLossMatrix(),
-                                           null,
-                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
-                                           sep,
-                                           ForesterUtil.LINE_SEPARATOR,
-                                           "Fitch Parsimony | Present | Domain Combinations",
-                                           "",
-                                           null,
-                                           all_pfams_encountered,
-                                           null,
-                                           "_fitch_present_dc" );
+                                           "_fitch_losses_dc",
+                                           tax_code_to_id_map );
+            //            writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
+            //                                           go_id_to_term_map,
+            //                                           go_namespace_limit,
+            //                                           true,
+            //                                           domain_parsimony.getGainLossMatrix(),
+            //                                           null,
+            //                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
+            //                                           sep,
+            //                                           ForesterUtil.LINE_SEPARATOR,
+            //                                           "Fitch Parsimony | Present | Domain Combinations",
+            //                                           "",
+            //                                           null,
+            //                                           all_pfams_encountered,
+            //                                           null,
+            //                                           "_fitch_present_dc",
+            //                                           tax_code_to_id_map );
             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
                                             go_id_to_term_map,
                                             outfile_name,
@@ -1015,7 +937,8 @@ public final class SurfacingUtil {
                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
                                                                      final Phylogeny phylogeny,
                                                                      final String parameters_str,
-                                                                     final Map<Species, MappingResults> mapping_results_map ) {
+                                                                     final Map<Species, MappingResults> mapping_results_map,
+                                                                     final boolean use_last_in_fitch_parsimony ) {
         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
         final String date_time = ForesterUtil.getCurrentDateTime();
         System.out.println();
@@ -1064,7 +987,8 @@ public final class SurfacingUtil {
         // -------------------------
         local_phylogeny_copy = phylogeny.copy();
         final String randomization = "no";
-        secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
+        secondary_features_parsimony
+                .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
         preparePhylogeny( local_phylogeny_copy,
                           secondary_features_parsimony,
                           date_time,
@@ -1083,58 +1007,62 @@ public final class SurfacingUtil {
                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
     }
 
-    public static void doit( final List<Protein> proteins,
-                             final List<DomainId> query_domain_ids_nc_order,
-                             final Writer out,
-                             final String separator,
-                             final String limit_to_species,
-                             final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
-        for( final Protein protein : proteins ) {
-            if ( ForesterUtil.isEmpty( limit_to_species )
-                    || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
-                if ( protein.contains( query_domain_ids_nc_order, true ) ) {
-                    out.write( protein.getSpecies().getSpeciesId() );
-                    out.write( separator );
-                    out.write( protein.getProteinId().getId() );
-                    out.write( separator );
-                    out.write( "[" );
-                    final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
-                    boolean first = true;
-                    for( final Domain domain : protein.getProteinDomains() ) {
-                        if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
-                            visited_domain_ids.add( domain.getDomainId() );
-                            if ( first ) {
-                                first = false;
-                            }
-                            else {
-                                out.write( " " );
-                            }
-                            out.write( domain.getDomainId().getId() );
-                            out.write( " {" );
-                            out.write( "" + domain.getTotalCount() );
-                            out.write( "}" );
-                        }
-                    }
-                    out.write( "]" );
-                    out.write( separator );
-                    if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
-                            .equals( SurfacingConstants.NONE ) ) ) {
-                        out.write( protein.getDescription() );
-                    }
-                    out.write( separator );
-                    if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
-                            .equals( SurfacingConstants.NONE ) ) ) {
-                        out.write( protein.getAccession() );
-                    }
-                    out.write( SurfacingConstants.NL );
-                }
-            }
+    public static void executePlusMinusAnalysis( final File output_file,
+                                                 final List<String> plus_minus_analysis_high_copy_base,
+                                                 final List<String> plus_minus_analysis_high_copy_target,
+                                                 final List<String> plus_minus_analysis_low_copy,
+                                                 final List<GenomeWideCombinableDomains> gwcd_list,
+                                                 final SortedMap<Species, List<Protein>> protein_lists_per_species,
+                                                 final Map<String, List<GoId>> domain_id_to_go_ids_map,
+                                                 final Map<GoId, GoTerm> go_id_to_term_map,
+                                                 final List<Object> plus_minus_analysis_numbers ) {
+        final Set<String> all_spec = new HashSet<String>();
+        for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+            all_spec.add( gwcd.getSpecies().getSpeciesId() );
+        }
+        final File html_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX_HTML );
+        final File plain_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX );
+        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 );
+        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();
+        try {
+            DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
+                                                                       protein_lists_per_species,
+                                                                       plus_minus_analysis_high_copy_base,
+                                                                       plus_minus_analysis_high_copy_target,
+                                                                       plus_minus_analysis_low_copy,
+                                                                       min_diff,
+                                                                       factor,
+                                                                       plain_out_dom,
+                                                                       html_out_dom,
+                                                                       html_out_dc,
+                                                                       domain_id_to_go_ids_map,
+                                                                       go_id_to_term_map,
+                                                                       all_domains_go_ids_out_dom,
+                                                                       passing_domains_go_ids_out_dom,
+                                                                       proteins_file_base );
         }
-        out.flush();
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+        }
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
+                + html_out_dom + "\"" );
+        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 \""
+                + all_domains_go_ids_out_dom + "\"" );
     }
 
     public static void extractProteinNames( final List<Protein> proteins,
-                                            final List<DomainId> query_domain_ids_nc_order,
+                                            final List<String> query_domain_ids_nc_order,
                                             final Writer out,
                                             final String separator,
                                             final String limit_to_species ) throws IOException {
@@ -1147,7 +1075,7 @@ public final class SurfacingUtil {
                     out.write( protein.getProteinId().getId() );
                     out.write( separator );
                     out.write( "[" );
-                    final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
+                    final Set<String> visited_domain_ids = new HashSet<String>();
                     boolean first = true;
                     for( final Domain domain : protein.getProteinDomains() ) {
                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
@@ -1158,7 +1086,7 @@ public final class SurfacingUtil {
                             else {
                                 out.write( " " );
                             }
-                            out.write( domain.getDomainId().getId() );
+                            out.write( domain.getDomainId() );
                             out.write( " {" );
                             out.write( "" + domain.getTotalCount() );
                             out.write( "}" );
@@ -1183,13 +1111,14 @@ public final class SurfacingUtil {
     }
 
     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
-                                            final DomainId domain_id,
+                                            final String domain_id,
                                             final Writer out,
                                             final String separator,
                                             final String limit_to_species,
                                             final double domain_e_cutoff ) throws IOException {
-        System.out.println( "Per domain E-value: " + domain_e_cutoff );
+        //System.out.println( "Per domain E-value: " + domain_e_cutoff );
         for( final Species species : protein_lists_per_species.keySet() ) {
+            //System.out.println( species + ":" );
             for( final Protein protein : protein_lists_per_species.get( species ) ) {
                 if ( ForesterUtil.isEmpty( limit_to_species )
                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
@@ -1201,34 +1130,33 @@ public final class SurfacingUtil {
                         out.write( separator );
                         out.write( domain_id.toString() );
                         out.write( separator );
+                        int prev_to = -1;
                         for( final Domain domain : domains ) {
-                            if ( domain_e_cutoff < 0 || domain.getPerDomainEvalue() <= domain_e_cutoff ) {
-                                 out.write( "/" );
-                                 out.write( domain.getFrom() + "-" + domain.getTo() );
+                            if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
+                                out.write( "/" );
+                                out.write( domain.getFrom() + "-" + domain.getTo() );
+                                if ( prev_to >= 0 ) {
+                                    final int l = domain.getFrom() - prev_to;
+                                    // System.out.println( l );
+                                }
+                                prev_to = domain.getTo();
                             }
                         }
                         out.write( "/" );
                         out.write( separator );
-                        
                         final List<Domain> domain_list = new ArrayList<Domain>();
-                        
                         for( final Domain domain : protein.getProteinDomains() ) {
-                            if ( domain_e_cutoff < 0 || domain.getPerDomainEvalue() <= domain_e_cutoff ) {
+                            if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
                                 domain_list.add( domain );
                             }
                         }
-                        
-                        Domain domain_ary[] = new Domain[ domain_list.size() ];
-                        
+                        final Domain domain_ary[] = new Domain[ domain_list.size() ];
                         for( int i = 0; i < domain_list.size(); ++i ) {
                             domain_ary[ i ] = domain_list.get( i );
                         }
-                        
                         Arrays.sort( domain_ary, new DomainComparator( true ) );
-                       
                         out.write( "{" );
                         boolean first = true;
-                        
                         for( final Domain domain : domain_ary ) {
                             if ( first ) {
                                 first = false;
@@ -1237,7 +1165,7 @@ public final class SurfacingUtil {
                                 out.write( "," );
                             }
                             out.write( domain.getDomainId().toString() );
-                            out.write( ":" + domain.getFrom() +  "-" + domain.getTo() );
+                            out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
                             out.write( ":" + domain.getPerDomainEvalue() );
                         }
                         out.write( "}" );
@@ -1258,10 +1186,10 @@ public final class SurfacingUtil {
         out.flush();
     }
 
-    public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
-        final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
+    public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
+        final SortedSet<String> all_domains_ids = new TreeSet<String>();
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
-            final Set<DomainId> all_domains = gwcd.getAllDomainIds();
+            final Set<String> all_domains = gwcd.getAllDomainIds();
             //    for( final Domain domain : all_domains ) {
             all_domains_ids.addAll( all_domains );
             //    }
@@ -1274,7 +1202,7 @@ public final class SurfacingUtil {
         for( final Protein protein_domain_collection : protein_domain_collections ) {
             for( final Object name : protein_domain_collection.getProteinDomains() ) {
                 final BasicDomain protein_domain = ( BasicDomain ) name;
-                final String id = protein_domain.getDomainId().getId();
+                final String id = protein_domain.getDomainId();
                 if ( map.containsKey( id ) ) {
                     map.put( id, map.get( id ) + 1 );
                 }
@@ -1310,21 +1238,192 @@ public final class SurfacingUtil {
         return c;
     }
 
-    /**
-     * Returns true is Domain domain falls in an uninterrupted stretch of
-     * covered positions.
-     * 
-     * @param domain
-     * @param covered_positions
-     * @return
-     */
-    public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
-        for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
-            if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
-                return false;
-            }
+    public static void log( final String msg, final Writer w ) {
+        try {
+            w.write( msg );
+            w.write( ForesterUtil.LINE_SEPARATOR );
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
         }
-        return true;
+    }
+
+    public static Phylogeny[] obtainAndPreProcessIntrees( final File[] intree_files,
+                                                          final int number_of_genomes,
+                                                          final String[][] input_file_properties ) {
+        final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
+        int i = 0;
+        for( final File intree_file : intree_files ) {
+            Phylogeny intree = null;
+            final String error = ForesterUtil.isReadableFile( intree_file );
+            if ( !ForesterUtil.isEmpty( error ) ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
+                        + error );
+            }
+            try {
+                final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
+                        .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" );
+                }
+                else if ( p_array.length > 1 ) {
+                    ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+                            + "] 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 );
+            }
+            if ( ( intree == null ) || intree.isEmpty() ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+            }
+            if ( !intree.isRooted() ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+            }
+            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 + "]" );
+            }
+            final StringBuilder parent_names = new StringBuilder();
+            final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names );
+            if ( nodes_lacking_name > 0 ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
+                        + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
+            }
+            preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
+            if ( !intree.isCompletelyBinary() ) {
+                ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
+                        + "] is not completely binary" );
+            }
+            intrees[ i++ ] = intree;
+        }
+        return intrees;
+    }
+
+    public static Phylogeny obtainFirstIntree( final File intree_file ) {
+        Phylogeny intree = null;
+        final String error = ForesterUtil.isReadableFile( intree_file );
+        if ( !ForesterUtil.isEmpty( error ) ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: " + error );
+        }
+        try {
+            final Phylogeny[] phys = ParserBasedPhylogenyFactory.getInstance()
+                    .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" );
+            }
+            else if ( phys.length > 1 ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
+                        + "] contains more than one phylogeny in phyloXML format" );
+            }
+            intree = phys[ 0 ];
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file + "]: "
+                    + error );
+        }
+        if ( ( intree == null ) || intree.isEmpty() ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
+        }
+        if ( !intree.isRooted() ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
+        }
+        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();
+                }
+                if ( c == null ) {
+                    throw new IllegalArgumentException( "no color found for taxonomy 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 void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
+                                                          final SortedMap<String, Integer> domain_architecuture_counts,
+                                                          final int min_count,
+                                                          final File da_counts_outfile,
+                                                          final File unique_da_outfile ) {
+        checkForOutputFileWriteability( da_counts_outfile );
+        checkForOutputFileWriteability( unique_da_outfile );
+        try {
+            final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
+            final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
+            final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
+            while ( it.hasNext() ) {
+                final Map.Entry<String, Integer> e = it.next();
+                final String da = e.getKey();
+                final int count = e.getValue();
+                if ( count >= min_count ) {
+                    da_counts_out.write( da );
+                    da_counts_out.write( "\t" );
+                    da_counts_out.write( String.valueOf( count ) );
+                    da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
+                }
+                if ( count == 1 ) {
+                    final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
+                    while ( it2.hasNext() ) {
+                        final Map.Entry<String, Set<String>> e2 = it2.next();
+                        final String genome = e2.getKey();
+                        final Set<String> das = e2.getValue();
+                        if ( das.contains( da ) ) {
+                            unique_da_out.write( genome );
+                            unique_da_out.write( "\t" );
+                            unique_da_out.write( da );
+                            unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
+                        }
+                    }
+                }
+            }
+            unique_da_out.close();
+            da_counts_out.close();
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
+        //
     }
 
     public static void preparePhylogeny( final Phylogeny p,
@@ -1348,6 +1447,225 @@ public final class SurfacingUtil {
         p.setRooted( true );
     }
 
+    public static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
+                                                             final String[][] input_file_properties ) {
+        final String[] genomes = new String[ input_file_properties.length ];
+        for( int i = 0; i < input_file_properties.length; ++i ) {
+            if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
+                        + "] is not unique in input tree " + intree.getName() );
+            }
+            genomes[ i ] = input_file_properties[ i ][ 1 ];
+        }
+        //
+        final PhylogenyNodeIterator it = intree.iteratorPostorder();
+        while ( it.hasNext() ) {
+            final PhylogenyNode n = it.next();
+            if ( ForesterUtil.isEmpty( n.getName() ) ) {
+                if ( n.getNodeData().isHasTaxonomy()
+                        && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
+                    n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
+                }
+                else if ( n.getNodeData().isHasTaxonomy()
+                        && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                    n.setName( n.getNodeData().getTaxonomy().getScientificName() );
+                }
+                else if ( n.getNodeData().isHasTaxonomy()
+                        && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
+                    n.setName( n.getNodeData().getTaxonomy().getCommonName() );
+                }
+                else {
+                    ForesterUtil
+                            .fatalError( surfacing.PRG_NAME,
+                                         "node with no name, scientific name, common name, or taxonomy code present" );
+                }
+            }
+        }
+        //
+        final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
+        if ( igns.size() > 0 ) {
+            System.out.println( "Not using the following " + igns.size() + " nodes:" );
+            for( int i = 0; i < igns.size(); ++i ) {
+                System.out.println( " " + i + ": " + igns.get( i ) );
+            }
+            System.out.println( "--" );
+        }
+        for( final String[] input_file_propertie : input_file_properties ) {
+            try {
+                intree.getNode( input_file_propertie[ 1 ] );
+            }
+            catch ( final IllegalArgumentException e ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
+                        + "] not present/not unique in input tree" );
+            }
+        }
+    }
+
+    public static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
+                                                                final Writer log_writer ) {
+        int sum = 0;
+        for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
+            sum += entry.getValue();
+        }
+        final double percentage = ( 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) ) / sum;
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
+        log( "Percentage of multidomain proteins:            : " + percentage + "%", log_writer );
+    }
+
+    public static void processFilter( final File filter_file, final SortedSet<String> filter ) {
+        SortedSet<String> filter_str = null;
+        try {
+            filter_str = ForesterUtil.file2set( filter_file );
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        if ( filter_str != null ) {
+            for( final String string : filter_str ) {
+                filter.add( string );
+            }
+        }
+        if ( surfacing.VERBOSE ) {
+            System.out.println( "Filter:" );
+            for( final String domainId : filter ) {
+                System.out.println( domainId );
+            }
+        }
+    }
+
+    public static String[][] processInputGenomesFile( final File input_genomes ) {
+        String[][] input_file_properties = null;
+        try {
+            input_file_properties = ForesterUtil.file22dArray( input_genomes );
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                     "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
+                                             + e.getLocalizedMessage() );
+        }
+        final Set<String> specs = new HashSet<String>();
+        final Set<String> paths = new HashSet<String>();
+        for( int i = 0; i < input_file_properties.length; ++i ) {
+            if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: "
+                        + input_file_properties[ i ][ 1 ] );
+            }
+            if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ]
+                        + " is not unique" );
+            }
+            specs.add( input_file_properties[ i ][ 1 ] );
+            if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ]
+                        + " is not unique" );
+            }
+            paths.add( input_file_properties[ i ][ 0 ] );
+            final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
+            if ( !ForesterUtil.isEmpty( error ) ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, error );
+            }
+        }
+        return input_file_properties;
+    }
+
+    public static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
+                                                       final List<String> high_copy_base,
+                                                       final List<String> high_copy_target,
+                                                       final List<String> low_copy,
+                                                       final List<Object> numbers ) {
+        if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+            if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
+                        + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
+            }
+            final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
+            final String msg = ForesterUtil.isReadableFile( plus_minus_file );
+            if ( !ForesterUtil.isEmpty( msg ) ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
+            }
+            processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
+        }
+    }
+
+    // First numbers is minimal difference, second is factor.
+    public static void processPlusMinusFile( final File plus_minus_file,
+                                             final List<String> high_copy_base,
+                                             final List<String> high_copy_target,
+                                             final List<String> low_copy,
+                                             final List<Object> numbers ) {
+        Set<String> species_set = null;
+        int min_diff = surfacing.PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
+        double factor = surfacing.PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
+        try {
+            species_set = ForesterUtil.file2set( plus_minus_file );
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        if ( species_set != null ) {
+            for( final String species : species_set ) {
+                final String species_trimmed = species.substring( 1 );
+                if ( species.startsWith( "+" ) ) {
+                    if ( low_copy.contains( species_trimmed ) ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                                 "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
+                                                         + species_trimmed + "\"" );
+                    }
+                    high_copy_base.add( species_trimmed );
+                }
+                else if ( species.startsWith( "*" ) ) {
+                    if ( low_copy.contains( species_trimmed ) ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                                 "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
+                                                         + species_trimmed + "\"" );
+                    }
+                    high_copy_target.add( species_trimmed );
+                }
+                else if ( species.startsWith( "-" ) ) {
+                    if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                                 "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
+                                                         + species_trimmed + "\"" );
+                    }
+                    low_copy.add( species_trimmed );
+                }
+                else if ( species.startsWith( "$D" ) ) {
+                    try {
+                        min_diff = Integer.parseInt( species.substring( 3 ) );
+                    }
+                    catch ( final NumberFormatException e ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME,
+                                                 "could not parse integer value for minimal difference from: \""
+                                                         + species.substring( 3 ) + "\"" );
+                    }
+                }
+                else if ( species.startsWith( "$F" ) ) {
+                    try {
+                        factor = Double.parseDouble( species.substring( 3 ) );
+                    }
+                    catch ( final NumberFormatException e ) {
+                        ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
+                                + species.substring( 3 ) + "\"" );
+                    }
+                }
+                else if ( species.startsWith( "#" ) ) {
+                    // Comment, ignore.
+                }
+                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 + "\"" );
+                }
+                numbers.add( new Integer( min_diff + "" ) );
+                numbers.add( new Double( factor + "" ) );
+            }
+        }
+        else {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
+        }
+    }
+
     /*
      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
      * 
@@ -1367,7 +1685,7 @@ public final class SurfacingUtil {
         if ( domains.size() > 1 ) {
             final Map<String, Integer> counts = new HashMap<String, Integer>();
             for( final Domain domain : domains ) {
-                final String id = domain.getDomainId().getId();
+                final String id = domain.getDomainId();
                 if ( counts.containsKey( id ) ) {
                     counts.put( id, counts.get( id ) + 1 );
                 }
@@ -1384,24 +1702,24 @@ public final class SurfacingUtil {
                         domain_n = domains.get( j );
                         domain_c = domains.get( i );
                     }
-                    final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
+                    final String dc = domain_n.getDomainId() + domain_c.getDomainId();
                     if ( !dcs.contains( dc ) ) {
                         dcs.add( dc );
                         sb.append( protein.getSpecies() );
                         sb.append( separator );
                         sb.append( protein_id );
                         sb.append( separator );
-                        sb.append( domain_n.getDomainId().getId() );
+                        sb.append( domain_n.getDomainId() );
                         sb.append( separator );
-                        sb.append( domain_c.getDomainId().getId() );
+                        sb.append( domain_c.getDomainId() );
                         sb.append( separator );
                         sb.append( domain_n.getPerDomainEvalue() );
                         sb.append( separator );
                         sb.append( domain_c.getPerDomainEvalue() );
                         sb.append( separator );
-                        sb.append( counts.get( domain_n.getDomainId().getId() ) );
+                        sb.append( counts.get( domain_n.getDomainId() ) );
                         sb.append( separator );
-                        sb.append( counts.get( domain_c.getDomainId().getId() ) );
+                        sb.append( counts.get( domain_c.getDomainId() ) );
                         sb.append( ForesterUtil.LINE_SEPARATOR );
                     }
                 }
@@ -1412,7 +1730,7 @@ public final class SurfacingUtil {
             sb.append( separator );
             sb.append( protein_id );
             sb.append( separator );
-            sb.append( domains.get( 0 ).getDomainId().getId() );
+            sb.append( domains.get( 0 ).getDomainId() );
             sb.append( separator );
             sb.append( separator );
             sb.append( domains.get( 0 ).getPerDomainEvalue() );
@@ -1437,55 +1755,6 @@ public final class SurfacingUtil {
         return sb;
     }
 
-    /**
-     * 
-     * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
-     * domain with 0.3 is ignored
-     * 
-     * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
-     * 
-     * 
-     * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
-     * ignored
-     * 
-     * @param max_allowed_overlap
-     *            maximal allowed overlap (inclusive) to be still considered not
-     *            overlapping (zero or negative value to allow any overlap)
-     * @param remove_engulfed_domains
-     *            to remove domains which are completely engulfed by coverage of
-     *            domains with better support
-     * @param protein
-     * @return
-     */
-    public static Protein removeOverlappingDomains( final int max_allowed_overlap,
-                                                    final boolean remove_engulfed_domains,
-                                                    final Protein protein ) {
-        final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
-                .getSpeciesId(), protein.getLength() );
-        final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
-        final List<Boolean> covered_positions = new ArrayList<Boolean>();
-        for( final Domain domain : sorted ) {
-            if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
-                    && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
-                final int covered_positions_size = covered_positions.size();
-                for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
-                    covered_positions.add( false );
-                }
-                final int new_covered_positions_size = covered_positions.size();
-                for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
-                    if ( i < new_covered_positions_size ) {
-                        covered_positions.set( i, true );
-                    }
-                    else {
-                        covered_positions.add( true );
-                    }
-                }
-                pruned_protein.addProteinDomain( domain );
-            }
-        }
-        return pruned_protein;
-    }
-
     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
         final List<Domain> domains = new ArrayList<Domain>();
         for( final Domain d : protein.getProteinDomains() ) {
@@ -1495,17 +1764,26 @@ 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 );
+    public static int storeDomainArchitectures( final String genome,
+                                                final SortedMap<String, Set<String>> domain_architecutures,
+                                                final List<Protein> protein_list,
+                                                final Map<String, Integer> distinct_domain_architecuture_counts ) {
+        final Set<String> da = new HashSet<String>();
+        domain_architecutures.put( genome, da );
+        for( final Protein protein : protein_list ) {
+            final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
+            if ( !da.contains( da_str ) ) {
+                if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
+                    distinct_domain_architecuture_counts.put( da_str, 1 );
+                }
+                else {
+                    distinct_domain_architecuture_counts.put( da_str,
+                                                              distinct_domain_architecuture_counts.get( da_str ) + 1 );
+                }
+                da.add( da_str );
+            }
         }
-        final List<String> l = new ArrayList<String>( 2 );
-        l.add( s[ 0 ] );
-        l.add( s[ 1 ] );
-        return l;
+        return da.size();
     }
 
     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
@@ -1537,212 +1815,66 @@ public final class SurfacingUtil {
         }
     }
 
-    private static void writeAllEncounteredPfamsToFile( final Map<DomainId, 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 DomainId domain_id = new DomainId( 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;
+            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 + "\"" );
+    }
+
+    public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
+                                                            final CharacterStateMatrix.GainLossStates state,
+                                                            final String filename,
+                                                            final String indentifier_characters_separator,
+                                                            final String character_separator,
+                                                            final Map<String, String> descriptions ) {
+        final File outfile = new File( filename );
+        checkForOutputFileWriteability( outfile );
+        final SortedSet<String> sorted_ids = new TreeSet<String>();
+        for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
+            sorted_ids.add( matrix.getIdentifier( i ) );
+        }
+        try {
+            final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
+            for( final String id : sorted_ids ) {
+                out.write( indentifier_characters_separator );
+                out.write( "#" + id );
+                out.write( indentifier_characters_separator );
+                for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
+                    // Not nice:
+                    // using null to indicate either UNCHANGED_PRESENT or GAIN.
+                    if ( ( matrix.getState( id, c ) == state )
+                            || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
+                                    .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
+                        out.write( matrix.getCharacter( c ) );
+                        if ( ( descriptions != null ) && !descriptions.isEmpty()
+                                && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
+                            out.write( "\t" );
+                            out.write( descriptions.get( matrix.getCharacter( c ) ) );
                         }
-                    }
-                    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 ][ 0 ]
-                + 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 );
-            }
-            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 + "\"" );
-    }
-
-    public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
-                                                            final CharacterStateMatrix.GainLossStates state,
-                                                            final String filename,
-                                                            final String indentifier_characters_separator,
-                                                            final String character_separator,
-                                                            final Map<String, String> descriptions ) {
-        final File outfile = new File( filename );
-        checkForOutputFileWriteability( outfile );
-        final SortedSet<String> sorted_ids = new TreeSet<String>();
-        for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
-            sorted_ids.add( matrix.getIdentifier( i ) );
-        }
-        try {
-            final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
-            for( final String id : sorted_ids ) {
-                out.write( indentifier_characters_separator );
-                out.write( "#" + id );
-                out.write( indentifier_characters_separator );
-                for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
-                    // Not nice:
-                    // using null to indicate either UNCHANGED_PRESENT or GAIN.
-                    if ( ( matrix.getState( id, c ) == state )
-                            || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
-                                    .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
-                        out.write( matrix.getCharacter( c ) );
-                        if ( ( descriptions != null ) && !descriptions.isEmpty()
-                                && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
-                            out.write( "\t" );
-                            out.write( descriptions.get( matrix.getCharacter( c ) ) );
-                        }
-                        out.write( character_separator );
+                        out.write( character_separator );
                     }
                 }
             }
@@ -1800,7 +1932,7 @@ public final class SurfacingUtil {
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
     }
 
-    public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                       final Map<GoId, GoTerm> go_id_to_term_map,
                                                       final GoNameSpace go_namespace_limit,
                                                       final boolean domain_combinations,
@@ -1811,10 +1943,11 @@ public final class SurfacingUtil {
                                                       final String character_separator,
                                                       final String title_for_html,
                                                       final String prefix_for_html,
-                                                      final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
+                                                      final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
                                                       final SortedSet<String> all_pfams_encountered,
                                                       final SortedSet<String> pfams_gained_or_lost,
-                                                      final String suffix_for_per_node_events_file ) {
+                                                      final String suffix_for_per_node_events_file,
+                                                      final Map<String, Integer> tax_code_to_id_map ) {
         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
         }
@@ -1841,7 +1974,7 @@ 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 );
@@ -1875,7 +2008,7 @@ public final class SurfacingUtil {
                 out.write( SurfacingConstants.NL );
                 out.write( "<h2>" );
                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
-                writeTaxonomyLinks( out, id );
+                writeTaxonomyLinks( out, id, tax_code_to_id_map );
                 out.write( "</h2>" );
                 out.write( SurfacingConstants.NL );
                 out.write( "<table>" );
@@ -1955,88 +2088,1016 @@ public final class SurfacingUtil {
                         }
                     }
                 }
-                if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
-                    per_node_go_mapped_domain_gain_loss_outfile_writer.close();
-                    if ( per_node_counter < 1 ) {
-                        per_node_go_mapped_domain_gain_loss_outfile.delete();
-                    }
-                    per_node_counter = 0;
+                if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
+                    per_node_go_mapped_domain_gain_loss_outfile_writer.close();
+                    if ( per_node_counter < 1 ) {
+                        per_node_go_mapped_domain_gain_loss_outfile.delete();
+                    }
+                    per_node_counter = 0;
+                }
+                out.write( "</table>" );
+                out.write( SurfacingConstants.NL );
+                out.write( "<hr>" );
+                out.write( SurfacingConstants.NL );
+            } // for( final String id : sorted_ids ) {  
+            out.write( "</body>" );
+            out.write( SurfacingConstants.NL );
+            out.write( "</html>" );
+            out.write( SurfacingConstants.NL );
+            out.flush();
+            out.close();
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
+    }
+
+    public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
+                                                          final File output_dir,
+                                                          final Writer per_genome_domain_promiscuity_statistics_writer,
+                                                          final GenomeWideCombinableDomains gwcd,
+                                                          final int i,
+                                                          final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
+        File dc_outfile = new File( input_file_properties[ i ][ 1 ]
+                + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
+        if ( output_dir != null ) {
+            dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
+        }
+        checkForOutputFileWriteability( dc_outfile );
+        try {
+            final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
+            out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
+            out.close();
+        }
+        catch ( final IOException e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
+        }
+        final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
+        try {
+            per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
+            per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
+            if ( stats.getN() < 2 ) {
+                per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
+            }
+            else {
+                per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
+                        .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" );
+            per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
+            per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
+            final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
+            for( final String mpd : mpds ) {
+                per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
+            }
+            per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
+        }
+        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 + "\"" );
+        }
+    }
+
+    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,
+                                                      final 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 != '_' ) {
+                        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() ) {
+                ( ( 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 );
+            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( "Fungi", TaxonomyColors.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() ) {
+                ( ( 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;
+            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 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 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 );
                 }
-                out.write( "</table>" );
-                out.write( SurfacingConstants.NL );
-                out.write( "<hr>" );
-                out.write( SurfacingConstants.NL );
-            } // for( final String id : sorted_ids ) {  
-            out.write( "</body>" );
-            out.write( SurfacingConstants.NL );
-            out.write( "</html>" );
-            out.write( SurfacingConstants.NL );
-            out.flush();
-            out.close();
+            }
+            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.fatalError( surfacing.PRG_NAME, e.getMessage() );
+            ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
         }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
     }
 
-    public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
-                                                          final File output_dir,
-                                                          final Writer per_genome_domain_promiscuity_statistics_writer,
-                                                          final GenomeWideCombinableDomains gwcd,
-                                                          final int i,
-                                                          final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
-        File dc_outfile = new File( input_file_properties[ i ][ 0 ]
-                + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
-        if ( output_dir != null ) {
-            dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
-        }
-        checkForOutputFileWriteability( dc_outfile );
-        try {
-            final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
-            out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
-            out.close();
-        }
-        catch ( final IOException e ) {
-            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
-        }
-        final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
-        try {
-            per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
-            per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
-            if ( stats.getN() < 2 ) {
-                per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
-            }
-            else {
-                per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
-                        .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" );
-            per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
-            per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
-            final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
-            for( final DomainId mpd : mpds ) {
-                per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
-            }
-            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 + "\"" );
-        }
+    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<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                          final Map<GoId, GoTerm> go_id_to_term_map,
                                          final GoNameSpace go_namespace_limit,
                                          final Writer out,
@@ -2044,7 +3105,7 @@ public final class SurfacingUtil {
                                          final String domain_1,
                                          final String prefix_for_html,
                                          final String character_separator_for_non_html_output,
-                                         final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
+                                         final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
                                          final Set<GoId> all_go_ids ) throws IOException {
         boolean any_go_annotation_present = false;
         boolean first_has_no_go = false;
@@ -2057,22 +3118,20 @@ public final class SurfacingUtil {
             List<GoId> go_ids = null;
             boolean go_annotation_present = false;
             if ( d == 0 ) {
-                final DomainId domain_id = new DomainId( domain_0 );
-                if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
+                if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
                     go_annotation_present = true;
                     any_go_annotation_present = true;
-                    go_ids = domain_id_to_go_ids_map.get( domain_id );
+                    go_ids = domain_id_to_go_ids_map.get( domain_0 );
                 }
                 else {
                     first_has_no_go = true;
                 }
             }
             else {
-                final DomainId domain_id = new DomainId( domain_1 );
-                if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
+                if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
                     go_annotation_present = true;
                     any_go_annotation_present = true;
-                    go_ids = domain_id_to_go_ids_map.get( domain_id );
+                    go_ids = domain_id_to_go_ids_map.get( domain_1 );
                 }
             }
             if ( go_annotation_present ) {
@@ -2083,339 +3142,77 @@ public final class SurfacingUtil {
                         first = false;
                         writeDomainIdsToHtml( out,
                                               domain_0,
-                                              domain_1,
-                                              prefix_for_html,
-                                              domain_id_to_secondary_features_maps );
-                    }
-                    else {
-                        out.write( "<td></td>" );
-                    }
-                    if ( !go_id_to_term_map.containsKey( go_id ) ) {
-                        throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
-                    }
-                    final GoTerm go_term = go_id_to_term_map.get( go_id );
-                    if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
-                        // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
-                        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>" );
-                        out.write( "</td><td>" );
-                        out.write( go_term.getName() );
-                        if ( domain_count == 2 ) {
-                            out.write( " (" + d + ")" );
-                        }
-                        out.write( "</td><td>" );
-                        // out.write( top );
-                        // out.write( "</td><td>" );
-                        out.write( "[" );
-                        out.write( go_term.getGoNameSpace().toShortString() );
-                        out.write( "]" );
-                        out.write( "</td>" );
-                        if ( all_go_ids != null ) {
-                            all_go_ids.add( go_id );
-                        }
-                    }
-                    else {
-                        out.write( "<td>" );
-                        out.write( "</td><td>" );
-                        out.write( "</td><td>" );
-                        out.write( "</td><td>" );
-                        out.write( "</td>" );
-                    }
-                    out.write( "</tr>" );
-                    out.write( SurfacingConstants.NL );
-                }
-            }
-        } //  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 );
-            out.write( "<td>" );
-            out.write( "</td><td>" );
-            out.write( "</td><td>" );
-            out.write( "</td><td>" );
-            out.write( "</td>" );
-            out.write( "</tr>" );
-            out.write( SurfacingConstants.NL );
-        }
-    }
-
-    private static void writeDomainIdsToHtml( final Writer out,
-                                              final String domain_0,
-                                              final String domain_1,
-                                              final String prefix_for_detailed_html,
-                                              final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
-            throws IOException {
-        out.write( "<td>" );
-        if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
-            out.write( prefix_for_detailed_html );
-            out.write( " " );
-        }
-        out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
-        out.write( "</td>" );
-    }
-
-    public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
-                                                                       final StringBuilder html_title,
-                                                                       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.DomainSimilaritySortField sort_field,
-                                                                       final DomainSimilarity.DomainSimilarityScoring scoring,
-                                                                       final boolean verbose ) throws IOException {
-        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
-        String histogram_title = null;
-        switch ( sort_field ) {
-            case ABS_MAX_COUNTS_DIFFERENCE:
-                if ( treat_as_binary ) {
-                    histogram_title = "absolute counts difference:";
-                }
-                else {
-                    histogram_title = "absolute (maximal) counts difference:";
-                }
-                break;
-            case MAX_COUNTS_DIFFERENCE:
-                if ( treat_as_binary ) {
-                    histogram_title = "counts difference:";
-                }
-                else {
-                    histogram_title = "(maximal) counts difference:";
-                }
-                break;
-            case DOMAIN_ID:
-                histogram_title = "score mean:";
-                break;
-            case MIN:
-                histogram_title = "score minimum:";
-                break;
-            case MAX:
-                histogram_title = "score maximum:";
-                break;
-            case MAX_DIFFERENCE:
-                if ( treat_as_binary ) {
-                    histogram_title = "difference:";
-                }
-                else {
-                    histogram_title = "(maximal) difference:";
-                }
-                break;
-            case MEAN:
-                histogram_title = "score mean:";
-                break;
-            case SD:
-                histogram_title = "score standard deviation:";
-                break;
-            case SPECIES_COUNT:
-                histogram_title = "species number:";
-                break;
-            default:
-                throw new AssertionError( "Unknown sort field: " + sort_field );
-        }
-        for( final DomainSimilarity similarity : similarities ) {
-            switch ( sort_field ) {
-                case ABS_MAX_COUNTS_DIFFERENCE:
-                    stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
-                    break;
-                case MAX_COUNTS_DIFFERENCE:
-                    stats.addValue( similarity.getMaximalDifferenceInCounts() );
-                    break;
-                case DOMAIN_ID:
-                    stats.addValue( similarity.getMeanSimilarityScore() );
-                    break;
-                case MIN:
-                    stats.addValue( similarity.getMinimalSimilarityScore() );
-                    break;
-                case MAX:
-                    stats.addValue( similarity.getMaximalSimilarityScore() );
-                    break;
-                case MAX_DIFFERENCE:
-                    stats.addValue( similarity.getMaximalDifference() );
-                    break;
-                case MEAN:
-                    stats.addValue( similarity.getMeanSimilarityScore() );
-                    break;
-                case SD:
-                    stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
-                    break;
-                case SPECIES_COUNT:
-                    stats.addValue( similarity.getSpecies().size() );
-                    break;
-                default:
-                    throw new AssertionError( "Unknown sort field: " + sort_field );
-            }
-        }
-        //
-        // final HistogramData[] hists = new HistogramData[ 1 ];
-        //      
-        //        
-        // List<HistogramDataItem> data_items = new
-        // ArrayList<HistogramDataItem>();
-        // double[] values = stats.getDataAsDoubleArray();
-        // for( int i = 0; i < values.length; i++ ) {
-        // HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
-        // i ] );
-        // data_items.add( data_item );
-        // }
-        //        
-        //        
-        // HistogramData hd0 = new HistogramData( "name",
-        // data_items,
-        // null, 20,
-        // 40 );
-        //        
-        //        
-        //        
-        //        
-        // hists[ 0 ] = hd0;
-        //       
-        // final HistogramsFrame hf = new HistogramsFrame( hists );
-        // hf.setVisible( true );
-        //
-        AsciiHistogram histo = null;
-        if ( stats.getMin() < stats.getMin() ) {
-            histo = new AsciiHistogram( stats, histogram_title );
-        }
-        if ( verbose ) {
-            if ( histo != null ) {
-                System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
-            }
-            System.out.println();
-            System.out.println( "N                   : " + stats.getN() );
-            System.out.println( "Min                 : " + stats.getMin() );
-            System.out.println( "Max                 : " + stats.getMax() );
-            System.out.println( "Mean                : " + stats.arithmeticMean() );
-            if ( stats.getN() > 1 ) {
-                System.out.println( "SD                  : " + stats.sampleStandardDeviation() );
-            }
-            else {
-                System.out.println( "SD                  : n/a" );
-            }
-            System.out.println( "Median              : " + stats.median() );
-            if ( stats.getN() > 1 ) {
-                System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
-            }
-            else {
-                System.out.println( "Pearsonian skewness : n/a" );
-            }
-        }
-        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, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
-                    }
-                    else {
-                        addHtmlHead( w, "DCs (" + 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( "<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>" );
+                                              domain_1,
+                                              prefix_for_html,
+                                              domain_id_to_secondary_features_maps );
                     }
                     else {
-                        w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
+                        out.write( "<td></td>" );
                     }
-                    w.write( SurfacingConstants.NL );
-                    w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
-                    w.write( SurfacingConstants.NL );
-                    if ( stats.getN() > 1 ) {
-                        w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
+                    if ( !go_id_to_term_map.containsKey( go_id ) ) {
+                        throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
+                    }
+                    final GoTerm go_term = go_id_to_term_map.get( go_id );
+                    if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
+                        // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
+                        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>" );
+                        out.write( "</td><td>" );
+                        out.write( go_term.getName() );
+                        if ( domain_count == 2 ) {
+                            out.write( " (" + d + ")" );
+                        }
+                        out.write( "</td><td>" );
+                        // out.write( top );
+                        // out.write( "</td><td>" );
+                        out.write( "[" );
+                        out.write( go_term.getGoNameSpace().toShortString() );
+                        out.write( "]" );
+                        out.write( "</td>" );
+                        if ( all_go_ids != null ) {
+                            all_go_ids.add( go_id );
+                        }
                     }
                     else {
-                        w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
+                        out.write( "<td>" );
+                        out.write( "</td><td>" );
+                        out.write( "</td><td>" );
+                        out.write( "</td><td>" );
+                        out.write( "</td>" );
                     }
-                    w.write( SurfacingConstants.NL );
-                    w.write( "</table>" );
-                    w.write( SurfacingConstants.NL );
-                    w.write( "<br>" );
-                    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 );
-                }
-                break;
-        }
-        for( final Writer w : split_writers.values() ) {
-            w.write( SurfacingConstants.NL );
-        }
-        for( final DomainSimilarity similarity : similarities ) {
-            if ( ( species_order != null ) && !species_order.isEmpty() ) {
-                ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
-            }
-            if ( single_writer != null ) {
-                single_writer.write( similarity.toStringBuffer( print_option ).toString() );
-            }
-            else {
-                Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
-                        .toLowerCase().charAt( 0 ) );
-                if ( local_writer == null ) {
-                    local_writer = split_writers.get( '0' );
+                    out.write( "</tr>" );
+                    out.write( SurfacingConstants.NL );
                 }
-                local_writer.write( similarity.toStringBuffer( print_option ).toString() );
             }
-            for( final Writer w : split_writers.values() ) {
-                w.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( 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 );
+            out.write( "<td>" );
+            out.write( "</td><td>" );
+            out.write( "</td><td>" );
+            out.write( "</td><td>" );
+            out.write( "</td>" );
+            out.write( "</tr>" );
+            out.write( SurfacingConstants.NL );
         }
-        for( final Writer w : split_writers.values() ) {
-            w.close();
+    }
+
+    private static void writeDomainIdsToHtml( final Writer out,
+                                              final String domain_0,
+                                              final String domain_1,
+                                              final String prefix_for_detailed_html,
+                                              final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
+            throws IOException {
+        out.write( "<td>" );
+        if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
+            out.write( prefix_for_detailed_html );
+            out.write( " " );
         }
-        return stats;
+        out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
+        out.write( "</td>" );
     }
 
     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
@@ -2429,40 +3226,6 @@ 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 ) ) );
@@ -2479,37 +3242,6 @@ public final class SurfacingUtil {
         }
     }
 
-    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 writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
-        if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
-            final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
-            writer.write( " [" );
-            if ( matcher.matches() ) {
-                writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + 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.TOL_LINK + species
-                        + "\" target=\"taxonomy_window\">tol</a>" );
-            }
-            writer.write( "]" );
-        }
-    }
-
     private static void writeToNexus( final String outfile_name,
                                       final CharacterStateMatrix<BinaryStates> matrix,
                                       final Phylogeny phylogeny ) {
@@ -2547,91 +3279,6 @@ public final class SurfacingUtil {
                       phylogeny );
     }
 
-    public static void domainsPerProteinsStatistics( final String genome,
-                                                     final List<Protein> protein_list,
-                                                     final DescriptiveStatistics all_genomes_domains_per_potein_stats,
-                                                     final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
-                                                     final SortedSet<String> domains_which_are_always_single,
-                                                     final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
-                                                     final SortedSet<String> domains_which_never_single,
-                                                     final Writer writer ) {
-        final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
-        for( final Protein protein : protein_list ) {
-            final int domains = protein.getNumberOfProteinDomains();
-            //System.out.println( domains );
-            stats.addValue( domains );
-            all_genomes_domains_per_potein_stats.addValue( domains );
-            if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
-                all_genomes_domains_per_potein_histo.put( domains, 1 );
-            }
-            else {
-                all_genomes_domains_per_potein_histo.put( domains,
-                                                          1 + all_genomes_domains_per_potein_histo.get( domains ) );
-            }
-            if ( domains == 1 ) {
-                final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
-                if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
-                    if ( domains_which_never_single.contains( domain ) ) {
-                        domains_which_never_single.remove( domain );
-                        domains_which_are_sometimes_single_sometimes_not.add( domain );
-                    }
-                    else {
-                        domains_which_are_always_single.add( domain );
-                    }
-                }
-            }
-            else if ( domains > 1 ) {
-                for( final Domain d : protein.getProteinDomains() ) {
-                    final String domain = d.getDomainId().getId();
-                    // System.out.println( domain );
-                    if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
-                        if ( domains_which_are_always_single.contains( domain ) ) {
-                            domains_which_are_always_single.remove( domain );
-                            domains_which_are_sometimes_single_sometimes_not.add( domain );
-                        }
-                        else {
-                            domains_which_never_single.add( domain );
-                        }
-                    }
-                }
-            }
-        }
-        try {
-            writer.write( genome );
-            writer.write( "\t" );
-            if ( stats.getN() >= 1 ) {
-                writer.write( stats.arithmeticMean() + "" );
-                writer.write( "\t" );
-                if ( stats.getN() >= 2 ) {
-                    writer.write( stats.sampleStandardDeviation() + "" );
-                }
-                else {
-                    writer.write( "" );
-                }
-                writer.write( "\t" );
-                writer.write( stats.median() + "" );
-                writer.write( "\t" );
-                writer.write( stats.getN() + "" );
-                writer.write( "\t" );
-                writer.write( stats.getMin() + "" );
-                writer.write( "\t" );
-                writer.write( stats.getMax() + "" );
-            }
-            else {
-                writer.write( "\t" );
-                writer.write( "\t" );
-                writer.write( "\t" );
-                writer.write( "0" );
-                writer.write( "\t" );
-                writer.write( "\t" );
-            }
-            writer.write( "\n" );
-        }
-        catch ( final IOException e ) {
-            e.printStackTrace();
-        }
-    }
-
     final static class DomainComparator implements Comparator<Domain> {
 
         final private boolean _ascending;
@@ -2642,7 +3289,6 @@ public final class SurfacingUtil {
 
         @Override
         public final int compare( final Domain d0, final Domain d1 ) {
-
             if ( d0.getFrom() < d1.getFrom() ) {
                 return _ascending ? -1 : 1;
             }
@@ -2650,13 +3296,6 @@ public final class SurfacingUtil {
                 return _ascending ? 1 : -1;
             }
             return 0;
-
         }
-
     }
 }
-
-
-
-
-