X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=forester%2Fjava%2Fsrc%2Forg%2Fforester%2Fsurfacing%2FSurfacingUtil.java;h=ea51d190da7ae4d2cc19980eabf460ac71157233;hb=0b49b8e750b34d28a5989facdd8a7959870de996;hp=ebce1ccbead6a18b3d0de0e79286ee0fdbc2d534;hpb=6ec28d1a3a137c14c9647aec7b9e40b77fe968bf;p=jalview.git

diff --git a/forester/java/src/org/forester/surfacing/SurfacingUtil.java b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
index ebce1cc..ea51d19 100644
--- a/forester/java/src/org/forester/surfacing/SurfacingUtil.java
+++ b/forester/java/src/org/forester/surfacing/SurfacingUtil.java
@@ -26,6 +26,7 @@
 
 package org.forester.surfacing;
 
+import java.awt.Color;
 import java.io.BufferedWriter;
 import java.io.File;
 import java.io.FileWriter;
@@ -66,6 +67,8 @@ 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.phylogeny.Phylogeny;
 import org.forester.phylogeny.PhylogenyMethods;
@@ -74,48 +77,50 @@ 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.DomainSimilarity.PRINT_OPTION;
 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
-import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
 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_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 final static Map<String, String> _TAXCODE_TAXGROUP_MAP            = new HashMap<String, String>();
+    private static final Comparator<Domain>  ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
+
+        @Override
+        public int compare( final Domain d1,
+                            final Domain d2 ) {
+            if ( d1.getPerDomainEvalue() < d2
+                    .getPerDomainEvalue() ) {
+                return -1;
+            }
+            else if ( d1.getPerDomainEvalue() > d2
+                    .getPerDomainEvalue() ) {
+                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 ) {
@@ -174,16 +150,6 @@ public final class SurfacingUtil {
         return stats;
     }
 
-    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 ) ) {
@@ -191,6 +157,33 @@ public final class SurfacingUtil {
         }
     }
 
+    public static void checkWriteabilityForPairwiseComparisons( final DomainSimilarity.PRINT_OPTION domain_similarity_print_option,
+                                                                final String[][] input_file_properties,
+                                                                final String automated_pairwise_comparison_suffix,
+                                                                final File outdir ) {
+        for( int i = 0; i < input_file_properties.length; ++i ) {
+            for( int j = 0; j < i; ++j ) {
+                final String species_i = input_file_properties[ i ][ 1 ];
+                final String species_j = input_file_properties[ j ][ 1 ];
+                String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i
+                        + "_" + species_j + automated_pairwise_comparison_suffix;
+                switch ( domain_similarity_print_option ) {
+                    case HTML:
+                        if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
+                            pairwise_similarities_output_file_str += ".html";
+                        }
+                        break;
+                }
+                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,
@@ -205,24 +198,23 @@ public final class SurfacingUtil {
                         || ( !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 ) ) );
+                                                                   .obtainInstance( matrix.getCharacter( c ) ) );
                     }
                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
-                                .createInstance( matrix.getCharacter( c ) ) );
+                                                                   .obtainInstance( matrix.getCharacter( c ) ) );
                     }
                     else {
-                        all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
-                                .getCharacter( c ) ) );
+                        all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.obtainInstance( matrix
+                                                                                                                .getCharacter( c ) ) );
                     }
                 }
             }
         }
     }
 
-    public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
-        final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
-                .size() );
+    public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
+        final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
@@ -232,12 +224,12 @@ public final class SurfacingUtil {
         return domain_id_to_go_ids_map;
     }
 
-    public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
+    public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
             throws IOException {
         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
-        final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
+        final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
-            final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
+            final String domain_id = primary_table.getValue( 0, r );
             if ( !map.containsKey( domain_id ) ) {
                 map.put( domain_id, new HashSet<String>() );
             }
@@ -255,6 +247,103 @@ public final class SurfacingUtil {
         return phylogeny;
     }
 
+    public static StringBuilder createParametersAsString( final boolean ignore_dufs,
+                                                          final double ie_value_max,
+                                                          final double fs_e_value_max,
+                                                          final int max_allowed_overlap,
+                                                          final boolean no_engulfing_overlaps,
+                                                          final File cutoff_scores_file,
+                                                          final BinaryDomainCombination.DomainCombinationType dc_type ) {
+        final StringBuilder parameters_sb = new StringBuilder();
+        parameters_sb.append( "iE-value: " + ie_value_max );
+        parameters_sb.append( ", FS E-value: " + fs_e_value_max );
+        if ( cutoff_scores_file != null ) {
+            parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
+        }
+        else {
+            parameters_sb.append( ", Cutoff-scores-file: not-set" );
+        }
+        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(); ) {
@@ -288,26 +377,17 @@ public final class SurfacingUtil {
     }
 
     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" );
-        }
+                                                            final Detailedness detailedness ) {
         for( final DomainSimilarity domain_similarity : domain_similarities ) {
-            if ( domain_similarity instanceof PrintableDomainSimilarity ) {
-                final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
+            if ( domain_similarity instanceof DomainSimilarity ) {
+                final DomainSimilarity printable_domain_similarity = domain_similarity;
                 printable_domain_similarity.setDetailedness( detailedness );
-                printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
-                printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
-                printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
             }
         }
     }
 
     public static void doit( final List<Protein> proteins,
-                             final List<DomainId> query_domain_ids_nc_order,
+                             final List<String> query_domain_ids_nc_order,
                              final Writer out,
                              final String separator,
                              final String limit_to_species,
@@ -321,7 +401,7 @@ public final class SurfacingUtil {
                     out.write( protein.getProteinId().getId() );
                     out.write( separator );
                     out.write( "[" );
-                    final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
+                    final Set<String> visited_domain_ids = new HashSet<String>();
                     boolean first = true;
                     for( final Domain domain : protein.getProteinDomains() ) {
                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
@@ -332,7 +412,7 @@ public final class SurfacingUtil {
                             else {
                                 out.write( " " );
                             }
-                            out.write( domain.getDomainId().getId() );
+                            out.write( domain.getDomainId() );
                             out.write( " {" );
                             out.write( "" + domain.getTotalCount() );
                             out.write( "}" );
@@ -378,7 +458,7 @@ public final class SurfacingUtil {
                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
             }
             if ( domains == 1 ) {
-                final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
+                final String domain = protein.getProteinDomain( 0 ).getDomainId();
                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
                     if ( domains_which_never_single.contains( domain ) ) {
                         domains_which_never_single.remove( domain );
@@ -391,7 +471,7 @@ public final class SurfacingUtil {
             }
             else if ( domains > 1 ) {
                 for( final Domain d : protein.getProteinDomains() ) {
-                    final String domain = d.getDomainId().getId();
+                    final String domain = d.getDomainId();
                     // System.out.println( domain );
                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
                         if ( domains_which_are_always_single.contains( domain ) ) {
@@ -464,10 +544,6 @@ 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 );
@@ -501,23 +577,99 @@ 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();
     }
 
     /**
-     * 
-     * @param all_binary_domains_combination_lost_fitch 
-     * @param consider_directedness_and_adjacency_for_bin_combinations 
+     * 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 perform_dc_fich
+     * @param consider_directedness_and_adjacency_for_bin_combinations
      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
      * which were gained under unweighted (Fitch) parsimony.
      */
@@ -526,12 +678,12 @@ public final class SurfacingUtil {
                                                  final String outfile_name,
                                                  final DomainParsimonyCalculator domain_parsimony,
                                                  final Phylogeny phylogeny,
-                                                 final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+                                                 final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                  final Map<GoId, GoTerm> go_id_to_term_map,
                                                  final GoNameSpace go_namespace_limit,
                                                  final String parameters_str,
-                                                 final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
-                                                 final SortedSet<DomainId> positive_filter,
+                                                 final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
+                                                 final SortedSet<String> positive_filter,
                                                  final boolean output_binary_domain_combinations_for_graphs,
                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
@@ -540,7 +692,9 @@ public final class SurfacingUtil {
                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
                                                  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 write_to_nexus,
+                                                 final boolean use_last_in_fitch_parsimony,
+                                                 final boolean perform_dc_fich ) {
         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
         final String date_time = ForesterUtil.getCurrentDateTime();
         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
@@ -561,9 +715,9 @@ public final class SurfacingUtil {
             domain_parsimony.executeDolloParsimonyOnDomainPresence();
         }
         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
                                                            CharacterStateMatrix.GainLossStates.GAIN,
                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
@@ -577,7 +731,7 @@ public final class SurfacingUtil {
                                                            ForesterUtil.LINE_SEPARATOR,
                                                            null );
         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
-                + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
+                                                           + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
         //HTML:
         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
                                        go_id_to_term_map,
@@ -611,22 +765,22 @@ public final class SurfacingUtil {
                                        all_pfams_lost_as_domains,
                                        "_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 );
+        //        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,
@@ -634,7 +788,7 @@ public final class SurfacingUtil {
                           "dollo_on_domains_" + outfile_name,
                           parameters_str );
         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
-                + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+                                            + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
         try {
             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
@@ -643,7 +797,7 @@ public final class SurfacingUtil {
             e.printStackTrace();
             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
         }
-        if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
+        if ( perform_dc_fich && ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) ) {
             // FITCH DOMAIN COMBINATIONS
             // -------------------------
             local_phylogeny_l = phylogeny.copy();
@@ -653,28 +807,28 @@ 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 );
+                                             + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
-                    + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
+                                             + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
             SurfacingUtil
-                    .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
-                                                          CharacterStateMatrix.GainLossStates.GAIN,
-                                                          outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
-                                                          sep,
-                                                          ForesterUtil.LINE_SEPARATOR,
-                                                          null );
+            .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
+                                                  CharacterStateMatrix.GainLossStates.GAIN,
+                                                  outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
+                                                  sep,
+                                                  ForesterUtil.LINE_SEPARATOR,
+                                                  null );
             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
                                                                CharacterStateMatrix.GainLossStates.LOSS,
                                                                outfile_name
-                                                                       + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
+                                                               + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
                                                                sep,
                                                                ForesterUtil.LINE_SEPARATOR,
                                                                null );
             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
-                    + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
+                                                               + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
             if ( all_binary_domains_combination_gained_fitch != null ) {
                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
                                                                                     dc_type,
@@ -689,14 +843,14 @@ public final class SurfacingUtil {
             }
             if ( output_binary_domain_combinations_for_graphs ) {
                 SurfacingUtil
-                        .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
-                                                                                                           .getGainLossMatrix(),
-                                                                                                   null,
-                                                                                                   outfile_name
-                                                                                                           + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
-                                                                                                   sep,
-                                                                                                   ForesterUtil.LINE_SEPARATOR,
-                                                                                                   BinaryDomainCombination.OutputFormat.DOT );
+                .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
+                                                                                           .getGainLossMatrix(),
+                                                                                           null,
+                                                                                           outfile_name
+                                                                                           + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
+                                                                                           sep,
+                                                                                           ForesterUtil.LINE_SEPARATOR,
+                                                                                           BinaryDomainCombination.OutputFormat.DOT );
             }
             // HTML:
             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
@@ -731,22 +885,22 @@ public final class SurfacingUtil {
                                            all_pfams_lost_as_dom_combinations,
                                            "_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 );
+            //            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,
@@ -761,19 +915,19 @@ public final class SurfacingUtil {
                               date_time,
                               "Fitch parsimony on binary domain combination presence/absence randomization: "
                                       + randomization,
-                              "fitch_on_binary_domain_combinations_" + outfile_name,
-                              parameters_str );
+                                      "fitch_on_binary_domain_combinations_" + outfile_name,
+                                      parameters_str );
             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
-                    + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
+                                                + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
             calculateIndependentDomainCombinationGains( local_phylogeny_l,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
                                                         outfile_name
-                                                                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
+                                                        + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
@@ -787,7 +941,8 @@ 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();
@@ -797,33 +952,33 @@ public final class SurfacingUtil {
         Phylogeny local_phylogeny_copy = phylogeny.copy();
         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
-                + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
+                                         + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
         SurfacingUtil
-                .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
-                                                      CharacterStateMatrix.GainLossStates.GAIN,
-                                                      outfile_name
-                                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
-                                                      sep,
-                                                      ForesterUtil.LINE_SEPARATOR,
-                                                      null );
+        .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+                                              CharacterStateMatrix.GainLossStates.GAIN,
+                                              outfile_name
+                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
+                                              sep,
+                                              ForesterUtil.LINE_SEPARATOR,
+                                              null );
         SurfacingUtil
-                .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
-                                                      CharacterStateMatrix.GainLossStates.LOSS,
-                                                      outfile_name
-                                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
-                                                      sep,
-                                                      ForesterUtil.LINE_SEPARATOR,
-                                                      null );
+        .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+                                              CharacterStateMatrix.GainLossStates.LOSS,
+                                              outfile_name
+                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
+                                              sep,
+                                              ForesterUtil.LINE_SEPARATOR,
+                                              null );
         SurfacingUtil
-                .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
-                                                      null,
-                                                      outfile_name
-                                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
-                                                      sep,
-                                                      ForesterUtil.LINE_SEPARATOR,
-                                                      null );
+        .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
+                                              null,
+                                              outfile_name
+                                              + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
+                                              sep,
+                                              ForesterUtil.LINE_SEPARATOR,
+                                              null );
         preparePhylogeny( local_phylogeny_copy,
                           secondary_features_parsimony,
                           date_time,
@@ -831,32 +986,87 @@ public final class SurfacingUtil {
                           "dollo_on_secondary_features_" + outfile_name,
                           parameters_str );
         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
-                + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
+                                            + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
         // FITCH DOMAIN COMBINATIONS
         // -------------------------
         local_phylogeny_copy = phylogeny.copy();
         final String randomization = "no";
-        secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
+        secondary_features_parsimony
+        .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
         preparePhylogeny( local_phylogeny_copy,
                           secondary_features_parsimony,
                           date_time,
                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
                                   + randomization,
-                          "fitch_on_binary_domain_combinations_" + outfile_name,
-                          parameters_str );
+                                  "fitch_on_binary_domain_combinations_" + outfile_name,
+                                  parameters_str );
         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
-                + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
+                                            + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
-                + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
-                + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
-                + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
+                                                    + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
+                                                    + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
+                                                    + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
+    }
+
+    public static void executePlusMinusAnalysis( final File output_file,
+                                                 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 );
+        }
+        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 {
@@ -869,7 +1079,7 @@ public final class SurfacingUtil {
                     out.write( protein.getProteinId().getId() );
                     out.write( separator );
                     out.write( "[" );
-                    final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
+                    final Set<String> visited_domain_ids = new HashSet<String>();
                     boolean first = true;
                     for( final Domain domain : protein.getProteinDomains() ) {
                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
@@ -880,7 +1090,7 @@ public final class SurfacingUtil {
                             else {
                                 out.write( " " );
                             }
-                            out.write( domain.getDomainId().getId() );
+                            out.write( domain.getDomainId() );
                             out.write( " {" );
                             out.write( "" + domain.getTotalCount() );
                             out.write( "}" );
@@ -905,14 +1115,14 @@ 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 + ":" );
+            //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 ) ) {
@@ -931,7 +1141,7 @@ public final class SurfacingUtil {
                                 out.write( domain.getFrom() + "-" + domain.getTo() );
                                 if ( prev_to >= 0 ) {
                                     final int l = domain.getFrom() - prev_to;
-                                    System.out.println( l );
+                                    // System.out.println( l );
                                 }
                                 prev_to = domain.getTo();
                             }
@@ -980,10 +1190,10 @@ public final class SurfacingUtil {
         out.flush();
     }
 
-    public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
-        final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
+    public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
+        final SortedSet<String> all_domains_ids = new TreeSet<String>();
         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
-            final Set<DomainId> all_domains = gwcd.getAllDomainIds();
+            final Set<String> all_domains = gwcd.getAllDomainIds();
             //    for( final Domain domain : all_domains ) {
             all_domains_ids.addAll( all_domains );
             //    }
@@ -996,7 +1206,7 @@ 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 );
                 }
@@ -1015,9 +1225,9 @@ public final class SurfacingUtil {
             final PhylogenyNode n = it.next();
             if ( ForesterUtil.isEmpty( n.getName() )
                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
-                            .getScientificName() ) )
-                    && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
-                            .getCommonName() ) ) ) {
+                                                                                   .getScientificName() ) )
+                                                                                   && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
+                                                                                                                                                  .getCommonName() ) ) ) {
                 if ( n.getParent() != null ) {
                     names.append( " " );
                     names.append( n.getParent().getName() );
@@ -1032,21 +1242,188 @@ 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() );
+        }
+    }
+
+    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 ];
         }
-        return true;
+        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();
+                //                }
+                final String group = obtainTaxonomyGroup( tax_code, phy );
+                final Color c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( group );
+                if ( c == null ) {
+                    throw new IllegalArgumentException( "no color found for taxonomy group \"" + group
+                                                        + "\" for code \"" + tax_code + "\"" );
+                }
+                final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
+                _TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex );
+            }
+            else {
+                throw new IllegalArgumentException( "unable to obtain color for code " + tax_code
+                                                    + " (tree is null or empty and code is not in map)" );
+            }
+        }
+        return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
+    }
+
+    public static String obtainTaxonomyGroup( final String tax_code, final Phylogeny species_tree )
+            throws IllegalArgumentException {
+        if ( !_TAXCODE_TAXGROUP_MAP.containsKey( tax_code ) ) {
+            if ( ( species_tree != null ) && !species_tree.isEmpty() ) {
+                final List<PhylogenyNode> nodes = species_tree.getNodesViaTaxonomyCode( tax_code );
+                if ( ( nodes == null ) || nodes.isEmpty() ) {
+                    throw new IllegalArgumentException( "code " + tax_code + " is not found" );
+                }
+                if ( nodes.size() != 1 ) {
+                    throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
+                }
+                PhylogenyNode n = nodes.get( 0 );
+                String group = null;
+                while ( n != null ) {
+                    if ( n.getNodeData().isHasTaxonomy()
+                            && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
+                        group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getNodeData().getTaxonomy()
+                                                                            .getScientificName() );
+                    }
+                    if ( ForesterUtil.isEmpty( group ) && !ForesterUtil.isEmpty( n.getName() ) ) {
+                        group = ForesterUtil.obtainNormalizedTaxonomyGroup( n.getName() );
+                    }
+                    if ( !ForesterUtil.isEmpty( group ) ) {
+                        break;
+                    }
+                    n = n.getParent();
+                }
+                if ( ForesterUtil.isEmpty( group ) ) {
+                    throw new IllegalArgumentException( "no group found for taxonomy code \"" + tax_code + "\"" );
+                }
+                _TAXCODE_TAXGROUP_MAP.put( tax_code, group );
+            }
+            else {
+                throw new IllegalArgumentException( "unable to obtain group for code " + tax_code
+                                                    + " (tree is null or empty and code is not in map)" );
+            }
+        }
+        return _TAXCODE_TAXGROUP_MAP.get( tax_code );
     }
 
     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
@@ -1117,10 +1494,229 @@ 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
-     * 
-     * 
+     *
+     *
      */
     static public StringBuffer proteinToDomainCombinations( final Protein protein,
                                                             final String protein_id,
@@ -1136,7 +1732,7 @@ public final class SurfacingUtil {
         if ( domains.size() > 1 ) {
             final Map<String, Integer> counts = new HashMap<String, Integer>();
             for( final Domain domain : domains ) {
-                final String id = domain.getDomainId().getId();
+                final String id = domain.getDomainId();
                 if ( counts.containsKey( id ) ) {
                     counts.put( id, counts.get( id ) + 1 );
                 }
@@ -1153,24 +1749,24 @@ public final class SurfacingUtil {
                         domain_n = domains.get( j );
                         domain_c = domains.get( i );
                     }
-                    final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
+                    final String dc = domain_n.getDomainId() + domain_c.getDomainId();
                     if ( !dcs.contains( dc ) ) {
                         dcs.add( dc );
                         sb.append( protein.getSpecies() );
                         sb.append( separator );
                         sb.append( protein_id );
                         sb.append( separator );
-                        sb.append( domain_n.getDomainId().getId() );
+                        sb.append( domain_n.getDomainId() );
                         sb.append( separator );
-                        sb.append( domain_c.getDomainId().getId() );
+                        sb.append( domain_c.getDomainId() );
                         sb.append( separator );
                         sb.append( domain_n.getPerDomainEvalue() );
                         sb.append( separator );
                         sb.append( domain_c.getPerDomainEvalue() );
                         sb.append( separator );
-                        sb.append( counts.get( domain_n.getDomainId().getId() ) );
+                        sb.append( counts.get( domain_n.getDomainId() ) );
                         sb.append( separator );
-                        sb.append( counts.get( domain_c.getDomainId().getId() ) );
+                        sb.append( counts.get( domain_c.getDomainId() ) );
                         sb.append( ForesterUtil.LINE_SEPARATOR );
                     }
                 }
@@ -1181,7 +1777,7 @@ 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() );
@@ -1206,55 +1802,6 @@ 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() ) {
@@ -1304,7 +1851,7 @@ public final class SurfacingUtil {
                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
                 if ( domains.size() > 0 ) {
                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
-                            + node.getName() + suffix_for_filename );
+                                                                             + node.getName() + suffix_for_filename );
                     for( final String domain : domains ) {
                         writer.write( domain );
                         writer.write( ForesterUtil.LINE_SEPARATOR );
@@ -1331,7 +1878,7 @@ public final class SurfacingUtil {
             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() );
+                               .toString() );
                 out_dot.write( SurfacingConstants.NL );
             }
             out_dot.close();
@@ -1339,9 +1886,16 @@ public final class SurfacingUtil {
         catch ( final IOException e ) {
             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
         }
-        ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
-                + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
-                + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+        if ( input_file_properties[ i ].length == 3 ) {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
+                    + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
+        }
+        else {
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
+                    + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
+                    + dc_outfile_dot + "\"" );
+        }
     }
 
     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
@@ -1413,7 +1967,7 @@ public final class SurfacingUtil {
                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
                         BinaryDomainCombination bdc = null;
                         try {
-                            bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
+                            bdc = BasicBinaryDomainCombination.obtainInstance( matrix.getCharacter( c ) );
                         }
                         catch ( final Exception e ) {
                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
@@ -1432,7 +1986,7 @@ public final class SurfacingUtil {
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
     }
 
-    public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                       final Map<GoId, GoTerm> go_id_to_term_map,
                                                       final GoNameSpace go_namespace_limit,
                                                       final boolean domain_combinations,
@@ -1443,7 +1997,7 @@ public final class SurfacingUtil {
                                                       final String character_separator,
                                                       final String title_for_html,
                                                       final String prefix_for_html,
-                                                      final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
+                                                      final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
                                                       final SortedSet<String> all_pfams_encountered,
                                                       final SortedSet<String> pfams_gained_or_lost,
                                                       final String suffix_for_per_node_events_file,
@@ -1474,7 +2028,7 @@ public final class SurfacingUtil {
             int per_node_counter = 0;
             out.write( "<html>" );
             out.write( SurfacingConstants.NL );
-            addHtmlHead( out, title_for_html );
+            writeHtmlHead( out, title_for_html );
             out.write( SurfacingConstants.NL );
             out.write( "<body>" );
             out.write( SurfacingConstants.NL );
@@ -1530,7 +2084,7 @@ public final class SurfacingUtil {
                 per_node_counter = 0;
                 if ( matrix.getNumberOfCharacters() > 0 ) {
                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
-                            + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
+                                                                            + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
@@ -1599,7 +2153,7 @@ public final class SurfacingUtil {
                 out.write( SurfacingConstants.NL );
                 out.write( "<hr>" );
                 out.write( SurfacingConstants.NL );
-            } // for( final String id : sorted_ids ) {  
+            } // for( final String id : sorted_ids ) {
             out.write( "</body>" );
             out.write( SurfacingConstants.NL );
             out.write( "</html>" );
@@ -1642,15 +2196,15 @@ public final class SurfacingUtil {
             }
             else {
                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
-                        .sampleStandardDeviation() ) + "\t" );
+                                                                                           .sampleStandardDeviation() ) + "\t" );
             }
             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
-            final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
-            for( final DomainId mpd : mpds ) {
-                per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
+            final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
+            for( final String mpd : mpds ) {
+                per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
             }
             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
         }
@@ -1669,127 +2223,20 @@ public final class SurfacingUtil {
         }
     }
 
-    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,
-                                                                       final Map<String, Integer> tax_code_to_id_map )
-            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 );
-            }
-        }
-        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" );
-            }
-        }
+    public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
+                                                      final StringBuilder html_title,
+                                                      final Writer simple_tab_writer,
+                                                      final Writer single_writer,
+                                                      Map<Character, Writer> split_writers,
+                                                      final SortedSet<DomainSimilarity> similarities,
+                                                      final boolean treat_as_binary,
+                                                      final List<Species> species_order,
+                                                      final DomainSimilarity.PRINT_OPTION print_option,
+                                                      final DomainSimilarity.DomainSimilarityScoring scoring,
+                                                      final boolean verbose,
+                                                      final Map<String, Integer> tax_code_to_id_map,
+                                                      final Phylogeny phy,
+                                                      final Set<String> pos_filter_doms ) throws IOException {
         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
             split_writers = new HashMap<Character, Writer>();
             split_writers.put( '_', single_writer );
@@ -1803,10 +2250,10 @@ public final class SurfacingUtil {
                     w.write( "<html>" );
                     w.write( SurfacingConstants.NL );
                     if ( key != '_' ) {
-                        addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
+                        writeHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
                     }
                     else {
-                        addHtmlHead( w, "DCs (" + html_title + ")" );
+                        writeHtmlHead( w, "DC analysis (" + html_title + ")" );
                     }
                     w.write( SurfacingConstants.NL );
                     w.write( "<body>" );
@@ -1814,75 +2261,123 @@ public final class SurfacingUtil {
                     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>" );
-                    }
-                    else {
-                        w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
-                    }
-                    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>" );
-                    }
-                    else {
-                        w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
-                    }
-                    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 );
+                    w.write( "<tr><td><b>Domains:</b></td></tr>" );
+                    w.write( SurfacingConstants.NL );
                 }
                 break;
         }
+        //
+        for( final DomainSimilarity similarity : similarities ) {
+            if ( ( species_order != null ) && !species_order.isEmpty() ) {
+                ( similarity ).setSpeciesOrder( species_order );
+            }
+            if ( single_writer != null ) {
+                if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+                    single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+                                         + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+                                         + "</span></a></b></td></tr>" );
+                }
+                else {
+                    single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+                            + similarity.getDomainId() + "</a></b></td></tr>" );
+                }
+                single_writer.write( SurfacingConstants.NL );
+            }
+            else {
+                Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
+                                                         .charAt( 0 ) );
+                if ( local_writer == null ) {
+                    local_writer = split_writers.get( '0' );
+                }
+                if ( !ForesterUtil.isEmpty( pos_filter_doms ) && pos_filter_doms.contains( similarity.getDomainId() ) ) {
+                    local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId()
+                                        + "\"><span style=\"color:#00ff00\">" + similarity.getDomainId()
+                                        + "</span></a></b></td></tr>" );
+                }
+                else {
+                    local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
+                            + similarity.getDomainId() + "</a></b></td></tr>" );
+                }
+                local_writer.write( SurfacingConstants.NL );
+            }
+        }
         for( final Writer w : split_writers.values() ) {
+            w.write( "</table>" );
+            w.write( SurfacingConstants.NL );
+            w.write( "<hr>" );
+            w.write( SurfacingConstants.NL );
+            //
+            w.write( "<table>" );
+            w.write( SurfacingConstants.NL );
+            w.write( "<tr><td><b>" );
+            w.write( "Species group colors:" );
+            w.write( "</b></td></tr>" );
+            w.write( SurfacingConstants.NL );
+            writeColorLabels( "Deuterostomia", TaxonomyColors.DEUTEROSTOMIA_COLOR, w );
+            writeColorLabels( "Protostomia", TaxonomyColors.PROTOSTOMIA_COLOR, w );
+            writeColorLabels( "Cnidaria", TaxonomyColors.CNIDARIA_COLOR, w );
+            writeColorLabels( "Placozoa", TaxonomyColors.PLACOZOA_COLOR, w );
+            writeColorLabels( "Ctenophora (comb jellies)", TaxonomyColors.CTENOPHORA_COLOR, w );
+            writeColorLabels( "Porifera (sponges)", TaxonomyColors.PORIFERA_COLOR, w );
+            writeColorLabels( "Choanoflagellida", TaxonomyColors.CHOANOFLAGELLIDA, w );
+            writeColorLabels( "Ichthyosporea & Filasterea", TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA, w );
+            writeColorLabels( "Dikarya (Ascomycota & Basidiomycota, so-called \"higher fungi\")",
+                              TaxonomyColors.DIKARYA_COLOR,
+                              w );
+            writeColorLabels( "other Fungi", TaxonomyColors.OTHER_FUNGI_COLOR, w );
+            writeColorLabels( "Nucleariidae and Fonticula group",
+                              TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR,
+                              w );
+            writeColorLabels( "Amoebozoa", TaxonomyColors.AMOEBOZOA_COLOR, w );
+            writeColorLabels( "Embryophyta (plants)", TaxonomyColors.EMBRYOPHYTA_COLOR, w );
+            writeColorLabels( "Chlorophyta (green algae)", TaxonomyColors.CHLOROPHYTA_COLOR, w );
+            writeColorLabels( "Rhodophyta (red algae)", TaxonomyColors.RHODOPHYTA_COLOR, w );
+            writeColorLabels( "Glaucocystophyce (Glaucophyta)", TaxonomyColors.GLAUCOPHYTA_COLOR, w );
+            writeColorLabels( "Hacrobia (Cryptophyta & Haptophyceae & Centroheliozoa)",
+                              TaxonomyColors.HACROBIA_COLOR,
+                              w );
+            writeColorLabels( "Stramenopiles (Chromophyta, heterokonts)", TaxonomyColors.STRAMENOPILES_COLOR, w );
+            writeColorLabels( "Alveolata", TaxonomyColors.ALVEOLATA_COLOR, w );
+            writeColorLabels( "Rhizaria", TaxonomyColors.RHIZARIA_COLOR, w );
+            writeColorLabels( "Excavata", TaxonomyColors.EXCAVATA_COLOR, w );
+            writeColorLabels( "Apusozoa", TaxonomyColors.APUSOZOA_COLOR, w );
+            writeColorLabels( "Archaea", TaxonomyColors.ARCHAEA_COLOR, w );
+            writeColorLabels( "Bacteria", TaxonomyColors.BACTERIA_COLOR, w );
+            w.write( "</table>" );
+            w.write( SurfacingConstants.NL );
+            //
+            w.write( "<hr>" );
+            w.write( SurfacingConstants.NL );
+            w.write( "<table>" );
             w.write( SurfacingConstants.NL );
         }
+        //
         for( final DomainSimilarity similarity : similarities ) {
             if ( ( species_order != null ) && !species_order.isEmpty() ) {
-                ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
+                ( 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 ).toString() );
+                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().getId().charAt( 0 ) + "" )
-                        .toLowerCase().charAt( 0 ) );
+                Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
+                                                         .charAt( 0 ) );
                 if ( local_writer == null ) {
                     local_writer = split_writers.get( '0' );
                 }
-                local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map ).toString() );
-            }
-            for( final Writer w : split_writers.values() ) {
-                w.write( SurfacingConstants.NL );
+                local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
+                local_writer.write( SurfacingConstants.NL );
             }
         }
         switch ( print_option ) {
@@ -1899,11 +2394,60 @@ public final class SurfacingUtil {
                     w.write( SurfacingConstants.NL );
                 }
                 break;
+            default:
+                break;
         }
         for( final Writer w : split_writers.values() ) {
             w.close();
         }
-        return stats;
+    }
+
+    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,
@@ -1952,6 +2496,57 @@ public final class SurfacingUtil {
         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
     }
 
+    public static void writePresentToNexus( final File output_file,
+                                            final File positive_filter_file,
+                                            final SortedSet<String> filter,
+                                            final List<GenomeWideCombinableDomains> gwcd_list ) {
+        try {
+            writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list,
+                                                                                                positive_filter_file == null ? null
+                                                                                                        : filter ),
+                                                                                                        output_file + surfacing.DOMAINS_PRESENT_NEXUS,
+                                                                                                        Format.NEXUS_BINARY );
+            writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
+                               output_file + surfacing.BDC_PRESENT_NEXUS,
+                               Format.NEXUS_BINARY );
+        }
+        catch ( final Exception e ) {
+            ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+        }
+    }
+
+    public static void writeProteinListsForAllSpecies( final File output_dir,
+                                                       final SortedMap<Species, List<Protein>> protein_lists_per_species,
+                                                       final List<GenomeWideCombinableDomains> gwcd_list,
+                                                       final double domain_e_cutoff,
+                                                       final Set<String> pos_filter_doms ) {
+        final SortedSet<String> all_domains = new TreeSet<String>();
+        for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
+            all_domains.addAll( gwcd.getAllDomainIds() );
+        }
+        for( final String domain : all_domains ) {
+            if ( !ForesterUtil.isEmpty( pos_filter_doms ) && !pos_filter_doms.contains( domain ) ) {
+                continue;
+            }
+            final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
+            checkForOutputFileWriteability( out );
+            try {
+                final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
+                extractProteinNames( protein_lists_per_species,
+                                     domain,
+                                     proteins_file_writer,
+                                     "\t",
+                                     surfacing.LIMIT_SPEC_FOR_PROT_EX,
+                                     domain_e_cutoff );
+                proteins_file_writer.close();
+            }
+            catch ( final IOException e ) {
+                ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
+            }
+            ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
+        }
+    }
+
     public static void writeTaxonomyLinks( final Writer writer,
                                            final String species,
                                            final Map<String, Integer> tax_code_to_id_map ) throws IOException {
@@ -1959,17 +2554,17 @@ public final class SurfacingUtil {
             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>" );
+                              + 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>" );
+                              + "\" target=\"taxonomy_window\">eol</a>" );
                 writer.write( "|" );
                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
-                        + "\" target=\"taxonomy_window\">scholar</a>" );
+                              + "\" target=\"taxonomy_window\">scholar</a>" );
                 writer.write( "|" );
                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
-                        + "\" target=\"taxonomy_window\">google</a>" );
+                              + "\" target=\"taxonomy_window\">google</a>" );
             }
             writer.write( "]" );
         }
@@ -2046,9 +2641,9 @@ public final class SurfacingUtil {
             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();
+            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;
@@ -2077,14 +2672,14 @@ public final class SurfacingUtil {
                         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() );
+                                                                                   .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() );
+                                                                                  .arithmeticMean() );
                 }
                 if ( domain_length_stats_by_domain != null ) {
                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
@@ -2092,9 +2687,9 @@ public final class SurfacingUtil {
                     }
                     final String[] ds = dc.split( "=" );
                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
-                            .get( ds[ 0 ] ).arithmeticMean() );
+                                                                                   .get( ds[ 0 ] ).arithmeticMean() );
                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
-                            .get( ds[ 1 ] ).arithmeticMean() );
+                                                                                   .get( ds[ 1 ] ).arithmeticMean() );
                 }
                 if ( count > 1 ) {
                     more_than_once.add( dc );
@@ -2282,16 +2877,19 @@ public final class SurfacingUtil {
                 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:" );
@@ -2336,32 +2934,32 @@ public final class SurfacingUtil {
                                                             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 );
+                                                                            + 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" );
+                                                                           + 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" );
+                                                                           + 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" );
+                                                                           + 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" );
+                                                                           + 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" );
+                                                                           + 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();
@@ -2370,15 +2968,51 @@ public final class SurfacingUtil {
     }
 
     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
-        final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
+        final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
-        for( final DomainId domain_id : cds.keySet() ) {
+        for( final String domain_id : cds.keySet() ) {
             final CombinableDomains cd = cds.get( domain_id );
             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
         }
         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 ) {
@@ -2392,13 +3026,13 @@ public final class SurfacingUtil {
         return l;
     }
 
-    private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                                         final Map<GoId, GoTerm> go_id_to_term_map,
                                                         final String outfile_name,
                                                         final SortedSet<String> all_pfams_encountered ) {
         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 );
+                                                                             + 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;
@@ -2420,7 +3054,7 @@ public final class SurfacingUtil {
             for( final String pfam : all_pfams_encountered ) {
                 all_pfams_encountered_writer.write( pfam );
                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
-                final DomainId domain_id = new DomainId( pfam );
+                final String domain_id = new String( pfam );
                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
                     ++pfams_with_mappings_counter;
                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
@@ -2467,10 +3101,10 @@ public final class SurfacingUtil {
             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 + "\"" );
+                                         + "] 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
-                    + "\"" );
+                                         + "] 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 + "\"" );
@@ -2501,7 +3135,7 @@ public final class SurfacingUtil {
             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() ) + "%]" );
+                                  + " [" + ( ( 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 + " ["
@@ -2530,7 +3164,16 @@ public final class SurfacingUtil {
         }
     }
 
-    private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
+    private final static void writeColorLabels( final String l, final Color c, final Writer w ) throws IOException {
+        w.write( "<tr><td><b><span style=\"color:" );
+        w.write( String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() ) );
+        w.write( "\">" );
+        w.write( l );
+        w.write( "</span></b></td></tr>" );
+        w.write( SurfacingConstants.NL );
+    }
+
+    private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
                                          final Map<GoId, GoTerm> go_id_to_term_map,
                                          final GoNameSpace go_namespace_limit,
                                          final Writer out,
@@ -2538,7 +3181,7 @@ 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;
@@ -2546,27 +3189,25 @@ public final class SurfacingUtil {
         if ( ForesterUtil.isEmpty( domain_1 ) ) {
             domain_count = 1;
         }
-        // The following has a difficult to understand logic.  
+        // The following has a difficult to understand logic.
         for( int d = 0; d < domain_count; ++d ) {
             List<GoId> go_ids = null;
             boolean go_annotation_present = false;
             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 ) {
@@ -2593,7 +3234,7 @@ public final class SurfacingUtil {
                         final String go_id_str = go_id.getId();
                         out.write( "<td>" );
                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
-                                + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
+                                   + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
                         out.write( "</td><td>" );
                         out.write( go_term.getName() );
                         if ( domain_count == 2 ) {
@@ -2621,7 +3262,7 @@ public final class SurfacingUtil {
                     out.write( SurfacingConstants.NL );
                 }
             }
-        } //  for( int d = 0; d < domain_count; ++d ) 
+        } //  for( int d = 0; d < domain_count; ++d )
         if ( !any_go_annotation_present ) {
             out.write( "<tr>" );
             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
@@ -2639,8 +3280,8 @@ public final class SurfacingUtil {
                                               final String domain_0,
                                               final String domain_1,
                                               final String prefix_for_detailed_html,
-                                              final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
-            throws IOException {
+                                              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 );
@@ -2670,7 +3311,7 @@ public final class SurfacingUtil {
             }
             writer.close();
             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
-                    + "]" );
+                                         + "]" );
         }
         catch ( final IOException e ) {
             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
@@ -2682,7 +3323,7 @@ public final class SurfacingUtil {
                                       final Phylogeny phylogeny ) {
         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
-                    + "] to nexus" );
+                                                + "] to nexus" );
         }
         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );