forester/java/src/org/forester/surfacing/SurfacingUtil.java

   1 // $Id:
   2 //
   3 // FORESTER -- software libraries and applications
   4 // for evolutionary biology research and applications.
   5 //
   6 // Copyright (C) 2008-2009 Christian M. Zmasek
   7 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   8 // All rights reserved
   9 //
  10 // This library is free software; you can redistribute it and/or
  11 // modify it under the terms of the GNU Lesser General Public
  12 // License as published by the Free Software Foundation; either
  13 // version 2.1 of the License, or (at your option) any later version.
  14 //
  15 // This library is distributed in the hope that it will be useful,
  16 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  17 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  18 // Lesser General Public License for more details.
  19 //
  20 // You should have received a copy of the GNU Lesser General Public
  21 // License along with this library; if not, write to the Free Software
  22 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  23 //
  24 // Contact: phylosoft @ gmail . com
  25 // WWW: https://sites.google.com/site/cmzmasek/home/software/forester
  26
  27 package org.forester.surfacing;
  28
  29 import java.awt.Color;
  30 import java.io.BufferedWriter;
  31 import java.io.File;
  32 import java.io.FileWriter;
  33 import java.io.IOException;
  34 import java.io.Writer;
  35 import java.text.DecimalFormat;
  36 import java.text.NumberFormat;
  37 import java.util.ArrayList;
  38 import java.util.Arrays;
  39 import java.util.Collections;
  40 import java.util.Comparator;
  41 import java.util.HashMap;
  42 import java.util.HashSet;
  43 import java.util.Iterator;
  44 import java.util.List;
  45 import java.util.Map;
  46 import java.util.Map.Entry;
  47 import java.util.PriorityQueue;
  48 import java.util.Set;
  49 import java.util.SortedMap;
  50 import java.util.SortedSet;
  51 import java.util.TreeMap;
  52 import java.util.TreeSet;
  53 import java.util.regex.Matcher;
  54 import java.util.regex.Pattern;
  55
  56 import org.forester.application.surfacing;
  57 import org.forester.evoinference.distance.NeighborJoining;
  58 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  59 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  60 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  61 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  62 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  63 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  64 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  65 import org.forester.go.GoId;
  66 import org.forester.go.GoNameSpace;
  67 import org.forester.go.GoTerm;
  68 import org.forester.go.PfamToGoMapping;
  69 import org.forester.io.parsers.nexus.NexusConstants;
  70 import org.forester.io.parsers.phyloxml.PhyloXmlUtil;
  71 import org.forester.io.parsers.util.ParserUtils;
  72 import org.forester.io.writers.PhylogenyWriter;
  73 import org.forester.phylogeny.Phylogeny;
  74 import org.forester.phylogeny.PhylogenyMethods;
  75 import org.forester.phylogeny.PhylogenyNode;
  76 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  77 import org.forester.phylogeny.data.BinaryCharacters;
  78 import org.forester.phylogeny.data.Confidence;
  79 import org.forester.phylogeny.data.Taxonomy;
  80 import org.forester.phylogeny.factories.ParserBasedPhylogenyFactory;
  81 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  82 import org.forester.protein.BasicDomain;
  83 import org.forester.protein.BasicProtein;
  84 import org.forester.protein.BinaryDomainCombination;
  85 import org.forester.protein.Domain;
  86 import org.forester.protein.Protein;
  87 import org.forester.species.Species;
  88 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  89 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  90 import org.forester.surfacing.PrintableDomainSimilarity.PRINT_OPTION;
  91 import org.forester.util.AsciiHistogram;
  92 import org.forester.util.BasicDescriptiveStatistics;
  93 import org.forester.util.BasicTable;
  94 import org.forester.util.BasicTableParser;
  95 import org.forester.util.CommandLineArguments;
  96 import org.forester.util.DescriptiveStatistics;
  97 import org.forester.util.ForesterUtil;
  98 import org.forester.util.TaxonomyColors;
  99
 100 public final class SurfacingUtil {
 101
 102     public final static Pattern              PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 103     private final static Map<String, String> _TAXCODE_HEXCOLORSTRING_MAP      = new HashMap<String, String>();
 104
 105
 106     private final static Map<String, String> _TAXCODE_TAXGROUP_MAP = new HashMap<String, String>();
 107
 108
 109     private static final Comparator<Domain>  ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
 110
 111                                                                                   @Override
 112                                                                                   public int compare( final Domain d1,
 113                                                                                                       final Domain d2 ) {
 114                                                                                       if ( d1.getPerSequenceEvalue() < d2
 115                                                                                               .getPerSequenceEvalue() ) {
 116                                                                                           return -1;
 117                                                                                       }
 118                                                                                       else if ( d1
 119                                                                                               .getPerSequenceEvalue() > d2
 120                                                                                               .getPerSequenceEvalue() ) {
 121                                                                                           return 1;
 122                                                                                       }
 123                                                                                       else {
 124                                                                                           return d1.compareTo( d2 );
 125                                                                                       }
 126                                                                                   }
 127                                                                               };
 128     private final static NumberFormat        FORMATTER_3                      = new DecimalFormat( "0.000" );
 129
 130     private SurfacingUtil() {
 131         // Hidden constructor.
 132     }
 133
 134     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 135                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 136         final SortedMap<String, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 137         for( final String domain_id : all_cd.keySet() ) {
 138             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 139         }
 140     }
 141
 142     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 143                                              final SortedSet<String> domain_ids ) {
 144         final SortedSet<String> domains = genome.getAllDomainIds();
 145         for( final String domain : domains ) {
 146             domain_ids.add( domain );
 147         }
 148     }
 149
 150     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 151         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 152         for( final DomainSimilarity similarity : similarities ) {
 153             stats.addValue( similarity.getMeanSimilarityScore() );
 154         }
 155         return stats;
 156     }
 157
 158     public static void checkForOutputFileWriteability( final File outfile ) {
 159         final String error = ForesterUtil.isWritableFile( outfile );
 160         if ( !ForesterUtil.isEmpty( error ) ) {
 161             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 162         }
 163     }
 164
 165     public static void checkWriteabilityForPairwiseComparisons( final PrintableDomainSimilarity.PRINT_OPTION domain_similarity_print_option,
 166                                                                 final String[][] input_file_properties,
 167                                                                 final String automated_pairwise_comparison_suffix,
 168                                                                 final File outdir ) {
 169         for( int i = 0; i < input_file_properties.length; ++i ) {
 170             for( int j = 0; j < i; ++j ) {
 171                 final String species_i = input_file_properties[ i ][ 1 ];
 172                 final String species_j = input_file_properties[ j ][ 1 ];
 173                 String pairwise_similarities_output_file_str = surfacing.PAIRWISE_DOMAIN_COMPARISONS_PREFIX + species_i
 174                         + "_" + species_j + automated_pairwise_comparison_suffix;
 175                 switch ( domain_similarity_print_option ) {
 176                     case HTML:
 177                         if ( !pairwise_similarities_output_file_str.endsWith( ".html" ) ) {
 178                             pairwise_similarities_output_file_str += ".html";
 179                         }
 180                         break;
 181                 }
 182                 final String error = ForesterUtil
 183                         .isWritableFile( new File( outdir == null ? pairwise_similarities_output_file_str : outdir
 184                                 + ForesterUtil.FILE_SEPARATOR + pairwise_similarities_output_file_str ) );
 185                 if ( !ForesterUtil.isEmpty( error ) ) {
 186                     ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 187                 }
 188             }
 189         }
 190     }
 191
 192     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 193                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 194                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 195                                                                                            final boolean get_gains ) {
 196         final SortedSet<String> sorted_ids = new TreeSet<String>();
 197         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 198             sorted_ids.add( matrix.getIdentifier( i ) );
 199         }
 200         for( final String id : sorted_ids ) {
 201             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 202                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 203                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 204                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 205                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 206                                 .createInstance( matrix.getCharacter( c ) ) );
 207                     }
 208                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 209                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 210                                 .createInstance( matrix.getCharacter( c ) ) );
 211                     }
 212                     else {
 213                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 214                                 .getCharacter( c ) ) );
 215                     }
 216                 }
 217             }
 218         }
 219     }
 220
 221     public static Map<String, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 222         final Map<String, List<GoId>> domain_id_to_go_ids_map = new HashMap<String, List<GoId>>( pfam_to_go_mappings.size() );
 223         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 224             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 225                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 226             }
 227             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 228         }
 229         return domain_id_to_go_ids_map;
 230     }
 231
 232     public static Map<String, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 233             throws IOException {
 234         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
 235         final Map<String, Set<String>> map = new TreeMap<String, Set<String>>();
 236         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 237             final String domain_id = primary_table.getValue( 0, r );
 238             if ( !map.containsKey( domain_id ) ) {
 239                 map.put( domain_id, new HashSet<String>() );
 240             }
 241             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 242         }
 243         return map;
 244     }
 245
 246     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 247         checkForOutputFileWriteability( nj_tree_outfile );
 248         final NeighborJoining nj = NeighborJoining.createInstance();
 249         final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
 250         phylogeny.setName( nj_tree_outfile.getName() );
 251         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 252         return phylogeny;
 253     }
 254
 255     public static StringBuilder createParametersAsString( final boolean ignore_dufs,
 256                                                           final double e_value_max,
 257                                                           final int max_allowed_overlap,
 258                                                           final boolean no_engulfing_overlaps,
 259                                                           final File cutoff_scores_file,
 260                                                           final BinaryDomainCombination.DomainCombinationType dc_type ) {
 261         final StringBuilder parameters_sb = new StringBuilder();
 262         parameters_sb.append( "E-value: " + e_value_max );
 263         if ( cutoff_scores_file != null ) {
 264             parameters_sb.append( ", Cutoff-scores-file: " + cutoff_scores_file );
 265         }
 266         else {
 267             parameters_sb.append( ", Cutoff-scores-file: not-set" );
 268         }
 269         if ( max_allowed_overlap != surfacing.MAX_ALLOWED_OVERLAP_DEFAULT ) {
 270             parameters_sb.append( ", Max-overlap: " + max_allowed_overlap );
 271         }
 272         else {
 273             parameters_sb.append( ", Max-overlap: not-set" );
 274         }
 275         if ( no_engulfing_overlaps ) {
 276             parameters_sb.append( ", Engulfing-overlaps: not-allowed" );
 277         }
 278         else {
 279             parameters_sb.append( ", Engulfing-overlaps: allowed" );
 280         }
 281         if ( ignore_dufs ) {
 282             parameters_sb.append( ", Ignore-dufs: true" );
 283         }
 284         else {
 285             parameters_sb.append( ", Ignore-dufs: false" );
 286         }
 287         parameters_sb.append( ", DC type (if applicable): " + dc_type );
 288         return parameters_sb;
 289     }
 290
 291     public static void createSplitWriters( final File out_dir,
 292                                            final String my_outfile,
 293                                            final Map<Character, Writer> split_writers ) throws IOException {
 294         split_writers.put( 'a', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 295                 + "_domains_A.html" ) ) );
 296         split_writers.put( 'b', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 297                 + "_domains_B.html" ) ) );
 298         split_writers.put( 'c', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 299                 + "_domains_C.html" ) ) );
 300         split_writers.put( 'd', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 301                 + "_domains_D.html" ) ) );
 302         split_writers.put( 'e', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 303                 + "_domains_E.html" ) ) );
 304         split_writers.put( 'f', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 305                 + "_domains_F.html" ) ) );
 306         split_writers.put( 'g', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 307                 + "_domains_G.html" ) ) );
 308         split_writers.put( 'h', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 309                 + "_domains_H.html" ) ) );
 310         split_writers.put( 'i', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 311                 + "_domains_I.html" ) ) );
 312         split_writers.put( 'j', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 313                 + "_domains_J.html" ) ) );
 314         split_writers.put( 'k', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 315                 + "_domains_K.html" ) ) );
 316         split_writers.put( 'l', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 317                 + "_domains_L.html" ) ) );
 318         split_writers.put( 'm', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 319                 + "_domains_M.html" ) ) );
 320         split_writers.put( 'n', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 321                 + "_domains_N.html" ) ) );
 322         split_writers.put( 'o', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 323                 + "_domains_O.html" ) ) );
 324         split_writers.put( 'p', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 325                 + "_domains_P.html" ) ) );
 326         split_writers.put( 'q', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 327                 + "_domains_Q.html" ) ) );
 328         split_writers.put( 'r', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 329                 + "_domains_R.html" ) ) );
 330         split_writers.put( 's', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 331                 + "_domains_S.html" ) ) );
 332         split_writers.put( 't', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 333                 + "_domains_T.html" ) ) );
 334         split_writers.put( 'u', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 335                 + "_domains_U.html" ) ) );
 336         split_writers.put( 'v', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 337                 + "_domains_V.html" ) ) );
 338         split_writers.put( 'w', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 339                 + "_domains_W.html" ) ) );
 340         split_writers.put( 'x', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 341                 + "_domains_X.html" ) ) );
 342         split_writers.put( 'y', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 343                 + "_domains_Y.html" ) ) );
 344         split_writers.put( 'z', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 345                 + "_domains_Z.html" ) ) );
 346         split_writers.put( '0', new BufferedWriter( new FileWriter( out_dir + ForesterUtil.FILE_SEPARATOR + my_outfile
 347                 + "_domains_0.html" ) ) );
 348     }
 349
 350     public static Map<String, Integer> createTaxCodeToIdMap( final Phylogeny phy ) {
 351         final Map<String, Integer> m = new HashMap<String, Integer>();
 352         for( final PhylogenyNodeIterator iter = phy.iteratorExternalForward(); iter.hasNext(); ) {
 353             final PhylogenyNode n = iter.next();
 354             if ( n.getNodeData().isHasTaxonomy() ) {
 355                 final Taxonomy t = n.getNodeData().getTaxonomy();
 356                 final String c = t.getTaxonomyCode();
 357                 if ( !ForesterUtil.isEmpty( c ) ) {
 358                     if ( n.getNodeData().getTaxonomy() == null ) {
 359                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 360                     }
 361                     final String id = n.getNodeData().getTaxonomy().getIdentifier().getValue();
 362                     if ( ForesterUtil.isEmpty( id ) ) {
 363                         ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy id for node " + n );
 364                     }
 365                     if ( m.containsKey( c ) ) {
 366                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy code " + c + " is not unique" );
 367                     }
 368                     final int iid = Integer.valueOf( id );
 369                     if ( m.containsValue( iid ) ) {
 370                         ForesterUtil.fatalError( surfacing.PRG_NAME, "taxonomy id " + iid + " is not unique" );
 371                     }
 372                     m.put( c, iid );
 373                 }
 374             }
 375             else {
 376                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no taxonomy for node " + n );
 377             }
 378         }
 379         return m;
 380     }
 381
 382     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 383                                                             final Detailedness detailedness ) {
 384         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 385             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 386                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 387                 printable_domain_similarity.setDetailedness( detailedness );
 388             }
 389         }
 390     }
 391
 392     public static void doit( final List<Protein> proteins,
 393                              final List<String> query_domain_ids_nc_order,
 394                              final Writer out,
 395                              final String separator,
 396                              final String limit_to_species,
 397                              final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
 398         for( final Protein protein : proteins ) {
 399             if ( ForesterUtil.isEmpty( limit_to_species )
 400                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
 401                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
 402                     out.write( protein.getSpecies().getSpeciesId() );
 403                     out.write( separator );
 404                     out.write( protein.getProteinId().getId() );
 405                     out.write( separator );
 406                     out.write( "[" );
 407                     final Set<String> visited_domain_ids = new HashSet<String>();
 408                     boolean first = true;
 409                     for( final Domain domain : protein.getProteinDomains() ) {
 410                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
 411                             visited_domain_ids.add( domain.getDomainId() );
 412                             if ( first ) {
 413                                 first = false;
 414                             }
 415                             else {
 416                                 out.write( " " );
 417                             }
 418                             out.write( domain.getDomainId() );
 419                             out.write( " {" );
 420                             out.write( "" + domain.getTotalCount() );
 421                             out.write( "}" );
 422                         }
 423                     }
 424                     out.write( "]" );
 425                     out.write( separator );
 426                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
 427                             .equals( SurfacingConstants.NONE ) ) ) {
 428                         out.write( protein.getDescription() );
 429                     }
 430                     out.write( separator );
 431                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
 432                             .equals( SurfacingConstants.NONE ) ) ) {
 433                         out.write( protein.getAccession() );
 434                     }
 435                     out.write( SurfacingConstants.NL );
 436                 }
 437             }
 438         }
 439         out.flush();
 440     }
 441
 442     public static void domainsPerProteinsStatistics( final String genome,
 443                                                      final List<Protein> protein_list,
 444                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
 445                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
 446                                                      final SortedSet<String> domains_which_are_always_single,
 447                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
 448                                                      final SortedSet<String> domains_which_never_single,
 449                                                      final Writer writer ) {
 450         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 451         for( final Protein protein : protein_list ) {
 452             final int domains = protein.getNumberOfProteinDomains();
 453             //System.out.println( domains );
 454             stats.addValue( domains );
 455             all_genomes_domains_per_potein_stats.addValue( domains );
 456             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
 457                 all_genomes_domains_per_potein_histo.put( domains, 1 );
 458             }
 459             else {
 460                 all_genomes_domains_per_potein_histo.put( domains,
 461                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
 462             }
 463             if ( domains == 1 ) {
 464                 final String domain = protein.getProteinDomain( 0 ).getDomainId();
 465                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 466                     if ( domains_which_never_single.contains( domain ) ) {
 467                         domains_which_never_single.remove( domain );
 468                         domains_which_are_sometimes_single_sometimes_not.add( domain );
 469                     }
 470                     else {
 471                         domains_which_are_always_single.add( domain );
 472                     }
 473                 }
 474             }
 475             else if ( domains > 1 ) {
 476                 for( final Domain d : protein.getProteinDomains() ) {
 477                     final String domain = d.getDomainId();
 478                     // System.out.println( domain );
 479                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
 480                         if ( domains_which_are_always_single.contains( domain ) ) {
 481                             domains_which_are_always_single.remove( domain );
 482                             domains_which_are_sometimes_single_sometimes_not.add( domain );
 483                         }
 484                         else {
 485                             domains_which_never_single.add( domain );
 486                         }
 487                     }
 488                 }
 489             }
 490         }
 491         try {
 492             writer.write( genome );
 493             writer.write( "\t" );
 494             if ( stats.getN() >= 1 ) {
 495                 writer.write( stats.arithmeticMean() + "" );
 496                 writer.write( "\t" );
 497                 if ( stats.getN() >= 2 ) {
 498                     writer.write( stats.sampleStandardDeviation() + "" );
 499                 }
 500                 else {
 501                     writer.write( "" );
 502                 }
 503                 writer.write( "\t" );
 504                 writer.write( stats.median() + "" );
 505                 writer.write( "\t" );
 506                 writer.write( stats.getN() + "" );
 507                 writer.write( "\t" );
 508                 writer.write( stats.getMin() + "" );
 509                 writer.write( "\t" );
 510                 writer.write( stats.getMax() + "" );
 511             }
 512             else {
 513                 writer.write( "\t" );
 514                 writer.write( "\t" );
 515                 writer.write( "\t" );
 516                 writer.write( "0" );
 517                 writer.write( "\t" );
 518                 writer.write( "\t" );
 519             }
 520             writer.write( "\n" );
 521         }
 522         catch ( final IOException e ) {
 523             e.printStackTrace();
 524         }
 525     }
 526
 527     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 528                                                     final int number_of_genomes,
 529                                                     final DomainLengthsTable domain_lengths_table,
 530                                                     final File outfile ) throws IOException {
 531         final DecimalFormat df = new DecimalFormat( "#.00" );
 532         checkForOutputFileWriteability( outfile );
 533         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 534         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 535         out.write( ForesterUtil.LINE_SEPARATOR );
 536         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 537         out.write( ForesterUtil.LINE_SEPARATOR );
 538         out.write( ForesterUtil.LINE_SEPARATOR );
 539         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 540         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 541         out.write( ForesterUtil.LINE_SEPARATOR );
 542         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 543             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 544             if ( species_list.size() > 0 ) {
 545                 out.write( domain_lengths.getDomainId() + "\t" );
 546                 for( final Species species : species_list ) {
 547                     out.write( species + "\t" );
 548                 }
 549                 out.write( ForesterUtil.LINE_SEPARATOR );
 550             }
 551         }
 552         out.write( ForesterUtil.LINE_SEPARATOR );
 553         out.write( ForesterUtil.LINE_SEPARATOR );
 554         out.write( "OUTLIER SPECIES (Z 1.0)" );
 555         out.write( ForesterUtil.LINE_SEPARATOR );
 556         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 557                 .calculateMeanBasedStatisticsForAllSpecies();
 558         out.write( stats_for_all_species.asSummary() );
 559         out.write( ForesterUtil.LINE_SEPARATOR );
 560         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 561         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 562         out.write( ForesterUtil.LINE_SEPARATOR );
 563         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 564         final double population_mean = stats_for_all_species.arithmeticMean();
 565         for( final Species species : domain_lengths_table.getSpecies() ) {
 566             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 567             final double z = ( x - population_mean ) / population_sd;
 568             out.write( species + "\t" + z );
 569             out.write( ForesterUtil.LINE_SEPARATOR );
 570         }
 571         out.write( ForesterUtil.LINE_SEPARATOR );
 572         for( final Species species : domain_lengths_table.getSpecies() ) {
 573             final DescriptiveStatistics stats_for_species = domain_lengths_table
 574                     .calculateMeanBasedStatisticsForSpecies( species );
 575             final double x = stats_for_species.arithmeticMean();
 576             final double z = ( x - population_mean ) / population_sd;
 577             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 578                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 579                 out.write( ForesterUtil.LINE_SEPARATOR );
 580             }
 581         }
 582         out.close();
 583         System.gc();
 584     }
 585
 586     /**
 587      * Warning: This side-effects 'all_bin_domain_combinations_encountered'!
 588      *
 589      *
 590      * @param output_file
 591      * @param all_bin_domain_combinations_changed
 592      * @param sum_of_all_domains_encountered
 593      * @param all_bin_domain_combinations_encountered
 594      * @param is_gains_analysis
 595      * @param protein_length_stats_by_dc
 596      * @throws IOException
 597      */
 598     public static void executeFitchGainsAnalysis( final File output_file,
 599                                                   final List<BinaryDomainCombination> all_bin_domain_combinations_changed,
 600                                                   final int sum_of_all_domains_encountered,
 601                                                   final SortedSet<BinaryDomainCombination> all_bin_domain_combinations_encountered,
 602                                                   final boolean is_gains_analysis ) throws IOException {
 603         checkForOutputFileWriteability( output_file );
 604         final Writer out = ForesterUtil.createBufferedWriter( output_file );
 605         final SortedMap<Object, Integer> bdc_to_counts = ForesterUtil
 606                 .listToSortedCountsMap( all_bin_domain_combinations_changed );
 607         final SortedSet<String> all_domains_in_combination_changed_more_than_once = new TreeSet<String>();
 608         final SortedSet<String> all_domains_in_combination_changed_only_once = new TreeSet<String>();
 609         int above_one = 0;
 610         int one = 0;
 611         for( final Object bdc_object : bdc_to_counts.keySet() ) {
 612             final BinaryDomainCombination bdc = ( BinaryDomainCombination ) bdc_object;
 613             final int count = bdc_to_counts.get( bdc_object );
 614             if ( count < 1 ) {
 615                 ForesterUtil.unexpectedFatalError( surfacing.PRG_NAME, "count < 1 " );
 616             }
 617             out.write( bdc + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 618             if ( count > 1 ) {
 619                 all_domains_in_combination_changed_more_than_once.add( bdc.getId0() );
 620                 all_domains_in_combination_changed_more_than_once.add( bdc.getId1() );
 621                 above_one++;
 622             }
 623             else if ( count == 1 ) {
 624                 all_domains_in_combination_changed_only_once.add( bdc.getId0() );
 625                 all_domains_in_combination_changed_only_once.add( bdc.getId1() );
 626                 one++;
 627             }
 628         }
 629         final int all = all_bin_domain_combinations_encountered.size();
 630         int never_lost = -1;
 631         if ( !is_gains_analysis ) {
 632             all_bin_domain_combinations_encountered.removeAll( all_bin_domain_combinations_changed );
 633             never_lost = all_bin_domain_combinations_encountered.size();
 634             for( final BinaryDomainCombination bdc : all_bin_domain_combinations_encountered ) {
 635                 out.write( bdc + "\t" + "0" + ForesterUtil.LINE_SEPARATOR );
 636             }
 637         }
 638         if ( is_gains_analysis ) {
 639             out.write( "Sum of all distinct domain combinations appearing once               : " + one
 640                     + ForesterUtil.LINE_SEPARATOR );
 641             out.write( "Sum of all distinct domain combinations appearing more than once     : " + above_one
 642                     + ForesterUtil.LINE_SEPARATOR );
 643             out.write( "Sum of all distinct domains in combinations apppearing only once     : "
 644                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 645             out.write( "Sum of all distinct domains in combinations apppearing more than once: "
 646                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 647         }
 648         else {
 649             out.write( "Sum of all distinct domain combinations never lost                   : " + never_lost
 650                     + ForesterUtil.LINE_SEPARATOR );
 651             out.write( "Sum of all distinct domain combinations lost once                    : " + one
 652                     + ForesterUtil.LINE_SEPARATOR );
 653             out.write( "Sum of all distinct domain combinations lost more than once          : " + above_one
 654                     + ForesterUtil.LINE_SEPARATOR );
 655             out.write( "Sum of all distinct domains in combinations lost only once           : "
 656                     + all_domains_in_combination_changed_only_once.size() + ForesterUtil.LINE_SEPARATOR );
 657             out.write( "Sum of all distinct domains in combinations lost more than once: "
 658                     + all_domains_in_combination_changed_more_than_once.size() + ForesterUtil.LINE_SEPARATOR );
 659         }
 660         out.write( "All binary combinations                                              : " + all
 661                 + ForesterUtil.LINE_SEPARATOR );
 662         out.write( "All domains                                                          : "
 663                 + sum_of_all_domains_encountered );
 664         out.close();
 665         ForesterUtil.programMessage( surfacing.PRG_NAME,
 666                                      "Wrote fitch domain combination dynamics counts analysis to \"" + output_file
 667                                              + "\"" );
 668     }
 669
 670     /**
 671      *
 672      * @param all_binary_domains_combination_lost_fitch
 673      * @param use_last_in_fitch_parsimony
 674      * @param consider_directedness_and_adjacency_for_bin_combinations
 675      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 676      * which were gained under unweighted (Fitch) parsimony.
 677      */
 678     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 679                                                  final boolean radomize_fitch_parsimony,
 680                                                  final String outfile_name,
 681                                                  final DomainParsimonyCalculator domain_parsimony,
 682                                                  final Phylogeny phylogeny,
 683                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
 684                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 685                                                  final GoNameSpace go_namespace_limit,
 686                                                  final String parameters_str,
 687                                                  final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
 688                                                  final SortedSet<String> positive_filter,
 689                                                  final boolean output_binary_domain_combinations_for_graphs,
 690                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 691                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 692                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 693                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 694                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 695                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain,
 696                                                  final Map<String, Integer> tax_code_to_id_map,
 697                                                  final boolean write_to_nexus,
 698                                                  final boolean use_last_in_fitch_parsimony ) {
 699         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 700         final String date_time = ForesterUtil.getCurrentDateTime();
 701         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 702         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 703         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 704         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 705         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 706         if ( write_to_nexus ) {
 707             writeToNexus( outfile_name, domain_parsimony, phylogeny );
 708         }
 709         // DOLLO DOMAINS
 710         // -------------
 711         Phylogeny local_phylogeny_l = phylogeny.copy();
 712         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 713             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 714         }
 715         else {
 716             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 717         }
 718         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 719                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 720         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 721                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 722         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 723                                                            CharacterStateMatrix.GainLossStates.GAIN,
 724                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 725                                                            sep,
 726                                                            ForesterUtil.LINE_SEPARATOR,
 727                                                            null );
 728         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 729                                                            CharacterStateMatrix.GainLossStates.LOSS,
 730                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 731                                                            sep,
 732                                                            ForesterUtil.LINE_SEPARATOR,
 733                                                            null );
 734         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 735                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 736         //HTML:
 737         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 738                                        go_id_to_term_map,
 739                                        go_namespace_limit,
 740                                        false,
 741                                        domain_parsimony.getGainLossMatrix(),
 742                                        CharacterStateMatrix.GainLossStates.GAIN,
 743                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 744                                        sep,
 745                                        ForesterUtil.LINE_SEPARATOR,
 746                                        "Dollo Parsimony | Gains | Domains",
 747                                        "+",
 748                                        domain_id_to_secondary_features_maps,
 749                                        all_pfams_encountered,
 750                                        all_pfams_gained_as_domains,
 751                                        "_dollo_gains_d",
 752                                        tax_code_to_id_map );
 753         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 754                                        go_id_to_term_map,
 755                                        go_namespace_limit,
 756                                        false,
 757                                        domain_parsimony.getGainLossMatrix(),
 758                                        CharacterStateMatrix.GainLossStates.LOSS,
 759                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 760                                        sep,
 761                                        ForesterUtil.LINE_SEPARATOR,
 762                                        "Dollo Parsimony | Losses | Domains",
 763                                        "-",
 764                                        domain_id_to_secondary_features_maps,
 765                                        all_pfams_encountered,
 766                                        all_pfams_lost_as_domains,
 767                                        "_dollo_losses_d",
 768                                        tax_code_to_id_map );
 769         //        writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 770         //                                       go_id_to_term_map,
 771         //                                       go_namespace_limit,
 772         //                                       false,
 773         //                                       domain_parsimony.getGainLossMatrix(),
 774         //                                       null,
 775         //                                       outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 776         //                                       sep,
 777         //                                       ForesterUtil.LINE_SEPARATOR,
 778         //                                       "Dollo Parsimony | Present | Domains",
 779         //                                       "",
 780         //                                       domain_id_to_secondary_features_maps,
 781         //                                       all_pfams_encountered,
 782         //                                       null,
 783         //                                       "_dollo_present_d",
 784         //                                       tax_code_to_id_map );
 785         preparePhylogeny( local_phylogeny_l,
 786                           domain_parsimony,
 787                           date_time,
 788                           "Dollo parsimony on domain presence/absence",
 789                           "dollo_on_domains_" + outfile_name,
 790                           parameters_str );
 791         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 792                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 793         try {
 794             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 795             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 796         }
 797         catch ( final IOException e ) {
 798             e.printStackTrace();
 799             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 800         }
 801         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 802             // FITCH DOMAIN COMBINATIONS
 803             // -------------------------
 804             local_phylogeny_l = phylogeny.copy();
 805             String randomization = "no";
 806             if ( radomize_fitch_parsimony ) {
 807                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 808                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 809             }
 810             else {
 811                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( use_last_in_fitch_parsimony );
 812             }
 813             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 814                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 815             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 816                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 817             SurfacingUtil
 818                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 819                                                           CharacterStateMatrix.GainLossStates.GAIN,
 820                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 821                                                           sep,
 822                                                           ForesterUtil.LINE_SEPARATOR,
 823                                                           null );
 824             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 825                                                                CharacterStateMatrix.GainLossStates.LOSS,
 826                                                                outfile_name
 827                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 828                                                                sep,
 829                                                                ForesterUtil.LINE_SEPARATOR,
 830                                                                null );
 831             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 832                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 833             if ( all_binary_domains_combination_gained_fitch != null ) {
 834                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 835                                                                                     dc_type,
 836                                                                                     all_binary_domains_combination_gained_fitch,
 837                                                                                     true );
 838             }
 839             if ( all_binary_domains_combination_lost_fitch != null ) {
 840                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 841                                                                                     dc_type,
 842                                                                                     all_binary_domains_combination_lost_fitch,
 843                                                                                     false );
 844             }
 845             if ( output_binary_domain_combinations_for_graphs ) {
 846                 SurfacingUtil
 847                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 848                                                                                                            .getGainLossMatrix(),
 849                                                                                                    null,
 850                                                                                                    outfile_name
 851                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 852                                                                                                    sep,
 853                                                                                                    ForesterUtil.LINE_SEPARATOR,
 854                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 855             }
 856             // HTML:
 857             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 858                                            go_id_to_term_map,
 859                                            go_namespace_limit,
 860                                            true,
 861                                            domain_parsimony.getGainLossMatrix(),
 862                                            CharacterStateMatrix.GainLossStates.GAIN,
 863                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
 864                                            sep,
 865                                            ForesterUtil.LINE_SEPARATOR,
 866                                            "Fitch Parsimony | Gains | Domain Combinations",
 867                                            "+",
 868                                            null,
 869                                            all_pfams_encountered,
 870                                            all_pfams_gained_as_dom_combinations,
 871                                            "_fitch_gains_dc",
 872                                            tax_code_to_id_map );
 873             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 874                                            go_id_to_term_map,
 875                                            go_namespace_limit,
 876                                            true,
 877                                            domain_parsimony.getGainLossMatrix(),
 878                                            CharacterStateMatrix.GainLossStates.LOSS,
 879                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
 880                                            sep,
 881                                            ForesterUtil.LINE_SEPARATOR,
 882                                            "Fitch Parsimony | Losses | Domain Combinations",
 883                                            "-",
 884                                            null,
 885                                            all_pfams_encountered,
 886                                            all_pfams_lost_as_dom_combinations,
 887                                            "_fitch_losses_dc",
 888                                            tax_code_to_id_map );
 889             //            writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 890             //                                           go_id_to_term_map,
 891             //                                           go_namespace_limit,
 892             //                                           true,
 893             //                                           domain_parsimony.getGainLossMatrix(),
 894             //                                           null,
 895             //                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
 896             //                                           sep,
 897             //                                           ForesterUtil.LINE_SEPARATOR,
 898             //                                           "Fitch Parsimony | Present | Domain Combinations",
 899             //                                           "",
 900             //                                           null,
 901             //                                           all_pfams_encountered,
 902             //                                           null,
 903             //                                           "_fitch_present_dc",
 904             //                                           tax_code_to_id_map );
 905             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
 906                                             go_id_to_term_map,
 907                                             outfile_name,
 908                                             all_pfams_encountered );
 909             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
 910             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
 911             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
 912                               all_pfams_gained_as_dom_combinations );
 913             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
 914             preparePhylogeny( local_phylogeny_l,
 915                               domain_parsimony,
 916                               date_time,
 917                               "Fitch parsimony on binary domain combination presence/absence randomization: "
 918                                       + randomization,
 919                               "fitch_on_binary_domain_combinations_" + outfile_name,
 920                               parameters_str );
 921             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 922                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
 923             calculateIndependentDomainCombinationGains( local_phylogeny_l,
 924                                                         outfile_name
 925                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
 926                                                         outfile_name
 927                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
 928                                                         outfile_name
 929                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
 930                                                         outfile_name
 931                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
 932                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
 933                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
 934                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
 935                                                         protein_length_stats_by_dc,
 936                                                         domain_number_stats_by_dc,
 937                                                         domain_length_stats_by_domain );
 938         }
 939     }
 940
 941     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
 942                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
 943                                                                      final Phylogeny phylogeny,
 944                                                                      final String parameters_str,
 945                                                                      final Map<Species, MappingResults> mapping_results_map,
 946                                                                      final boolean use_last_in_fitch_parsimony ) {
 947         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 948         final String date_time = ForesterUtil.getCurrentDateTime();
 949         System.out.println();
 950         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
 951                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
 952                       phylogeny );
 953         Phylogeny local_phylogeny_copy = phylogeny.copy();
 954         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
 955         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
 956                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 957         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
 958                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
 959         SurfacingUtil
 960                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 961                                                       CharacterStateMatrix.GainLossStates.GAIN,
 962                                                       outfile_name
 963                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
 964                                                       sep,
 965                                                       ForesterUtil.LINE_SEPARATOR,
 966                                                       null );
 967         SurfacingUtil
 968                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 969                                                       CharacterStateMatrix.GainLossStates.LOSS,
 970                                                       outfile_name
 971                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
 972                                                       sep,
 973                                                       ForesterUtil.LINE_SEPARATOR,
 974                                                       null );
 975         SurfacingUtil
 976                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
 977                                                       null,
 978                                                       outfile_name
 979                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
 980                                                       sep,
 981                                                       ForesterUtil.LINE_SEPARATOR,
 982                                                       null );
 983         preparePhylogeny( local_phylogeny_copy,
 984                           secondary_features_parsimony,
 985                           date_time,
 986                           "Dollo parsimony on secondary feature presence/absence",
 987                           "dollo_on_secondary_features_" + outfile_name,
 988                           parameters_str );
 989         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
 990                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 991         // FITCH DOMAIN COMBINATIONS
 992         // -------------------------
 993         local_phylogeny_copy = phylogeny.copy();
 994         final String randomization = "no";
 995         secondary_features_parsimony
 996                 .executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( use_last_in_fitch_parsimony );
 997         preparePhylogeny( local_phylogeny_copy,
 998                           secondary_features_parsimony,
 999                           date_time,
1000                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
1001                                   + randomization,
1002                           "fitch_on_binary_domain_combinations_" + outfile_name,
1003                           parameters_str );
1004         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
1005                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
1006         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
1007                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
1008                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
1009                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
1010                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
1011                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
1012                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
1013     }
1014
1015     public static void executePlusMinusAnalysis( final File output_file,
1016                                                  final List<String> plus_minus_analysis_high_copy_base,
1017                                                  final List<String> plus_minus_analysis_high_copy_target,
1018                                                  final List<String> plus_minus_analysis_low_copy,
1019                                                  final List<GenomeWideCombinableDomains> gwcd_list,
1020                                                  final SortedMap<Species, List<Protein>> protein_lists_per_species,
1021                                                  final Map<String, List<GoId>> domain_id_to_go_ids_map,
1022                                                  final Map<GoId, GoTerm> go_id_to_term_map,
1023                                                  final List<Object> plus_minus_analysis_numbers ) {
1024         final Set<String> all_spec = new HashSet<String>();
1025         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1026             all_spec.add( gwcd.getSpecies().getSpeciesId() );
1027         }
1028         final File html_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX_HTML );
1029         final File plain_out_dom = new File( output_file + surfacing.PLUS_MINUS_DOM_SUFFIX );
1030         final File html_out_dc = new File( output_file + surfacing.PLUS_MINUS_DC_SUFFIX_HTML );
1031         final File all_domains_go_ids_out_dom = new File( output_file + surfacing.PLUS_MINUS_ALL_GO_IDS_DOM_SUFFIX );
1032         final File passing_domains_go_ids_out_dom = new File( output_file
1033                 + surfacing.PLUS_MINUS_PASSING_GO_IDS_DOM_SUFFIX );
1034         final File proteins_file_base = new File( output_file + "" );
1035         final int min_diff = ( ( Integer ) plus_minus_analysis_numbers.get( 0 ) ).intValue();
1036         final double factor = ( ( Double ) plus_minus_analysis_numbers.get( 1 ) ).doubleValue();
1037         try {
1038             DomainCountsDifferenceUtil.calculateCopyNumberDifferences( gwcd_list,
1039                                                                        protein_lists_per_species,
1040                                                                        plus_minus_analysis_high_copy_base,
1041                                                                        plus_minus_analysis_high_copy_target,
1042                                                                        plus_minus_analysis_low_copy,
1043                                                                        min_diff,
1044                                                                        factor,
1045                                                                        plain_out_dom,
1046                                                                        html_out_dom,
1047                                                                        html_out_dc,
1048                                                                        domain_id_to_go_ids_map,
1049                                                                        go_id_to_term_map,
1050                                                                        all_domains_go_ids_out_dom,
1051                                                                        passing_domains_go_ids_out_dom,
1052                                                                        proteins_file_base );
1053         }
1054         catch ( final IOException e ) {
1055             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1056         }
1057         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
1058                 + html_out_dom + "\"" );
1059         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \""
1060                 + plain_out_dom + "\"" );
1061         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis results to \"" + html_out_dc
1062                 + "\"" );
1063         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based passing GO ids to \""
1064                 + passing_domains_go_ids_out_dom + "\"" );
1065         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote plus minus domain analysis based all GO ids to \""
1066                 + all_domains_go_ids_out_dom + "\"" );
1067     }
1068
1069     public static void extractProteinNames( final List<Protein> proteins,
1070                                             final List<String> query_domain_ids_nc_order,
1071                                             final Writer out,
1072                                             final String separator,
1073                                             final String limit_to_species ) throws IOException {
1074         for( final Protein protein : proteins ) {
1075             if ( ForesterUtil.isEmpty( limit_to_species )
1076                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1077                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1078                     out.write( protein.getSpecies().getSpeciesId() );
1079                     out.write( separator );
1080                     out.write( protein.getProteinId().getId() );
1081                     out.write( separator );
1082                     out.write( "[" );
1083                     final Set<String> visited_domain_ids = new HashSet<String>();
1084                     boolean first = true;
1085                     for( final Domain domain : protein.getProteinDomains() ) {
1086                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1087                             visited_domain_ids.add( domain.getDomainId() );
1088                             if ( first ) {
1089                                 first = false;
1090                             }
1091                             else {
1092                                 out.write( " " );
1093                             }
1094                             out.write( domain.getDomainId() );
1095                             out.write( " {" );
1096                             out.write( "" + domain.getTotalCount() );
1097                             out.write( "}" );
1098                         }
1099                     }
1100                     out.write( "]" );
1101                     out.write( separator );
1102                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1103                             .equals( SurfacingConstants.NONE ) ) ) {
1104                         out.write( protein.getDescription() );
1105                     }
1106                     out.write( separator );
1107                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1108                             .equals( SurfacingConstants.NONE ) ) ) {
1109                         out.write( protein.getAccession() );
1110                     }
1111                     out.write( SurfacingConstants.NL );
1112                 }
1113             }
1114         }
1115         out.flush();
1116     }
1117
1118     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
1119                                             final String domain_id,
1120                                             final Writer out,
1121                                             final String separator,
1122                                             final String limit_to_species,
1123                                             final double domain_e_cutoff ) throws IOException {
1124         //System.out.println( "Per domain E-value: " + domain_e_cutoff );
1125         for( final Species species : protein_lists_per_species.keySet() ) {
1126             //System.out.println( species + ":" );
1127             for( final Protein protein : protein_lists_per_species.get( species ) ) {
1128                 if ( ForesterUtil.isEmpty( limit_to_species )
1129                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1130                     final List<Domain> domains = protein.getProteinDomains( domain_id );
1131                     if ( domains.size() > 0 ) {
1132                         out.write( protein.getSpecies().getSpeciesId() );
1133                         out.write( separator );
1134                         out.write( protein.getProteinId().getId() );
1135                         out.write( separator );
1136                         out.write( domain_id.toString() );
1137                         out.write( separator );
1138                         int prev_to = -1;
1139                         for( final Domain domain : domains ) {
1140                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
1141                                 out.write( "/" );
1142                                 out.write( domain.getFrom() + "-" + domain.getTo() );
1143                                 if ( prev_to >= 0 ) {
1144                                     final int l = domain.getFrom() - prev_to;
1145                                     // System.out.println( l );
1146                                 }
1147                                 prev_to = domain.getTo();
1148                             }
1149                         }
1150                         out.write( "/" );
1151                         out.write( separator );
1152                         final List<Domain> domain_list = new ArrayList<Domain>();
1153                         for( final Domain domain : protein.getProteinDomains() ) {
1154                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
1155                                 domain_list.add( domain );
1156                             }
1157                         }
1158                         final Domain domain_ary[] = new Domain[ domain_list.size() ];
1159                         for( int i = 0; i < domain_list.size(); ++i ) {
1160                             domain_ary[ i ] = domain_list.get( i );
1161                         }
1162                         Arrays.sort( domain_ary, new DomainComparator( true ) );
1163                         out.write( "{" );
1164                         boolean first = true;
1165                         for( final Domain domain : domain_ary ) {
1166                             if ( first ) {
1167                                 first = false;
1168                             }
1169                             else {
1170                                 out.write( "," );
1171                             }
1172                             out.write( domain.getDomainId().toString() );
1173                             out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
1174                             out.write( ":" + domain.getPerDomainEvalue() );
1175                         }
1176                         out.write( "}" );
1177                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1178                                 .equals( SurfacingConstants.NONE ) ) ) {
1179                             out.write( protein.getDescription() );
1180                         }
1181                         out.write( separator );
1182                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1183                                 .equals( SurfacingConstants.NONE ) ) ) {
1184                             out.write( protein.getAccession() );
1185                         }
1186                         out.write( SurfacingConstants.NL );
1187                     }
1188                 }
1189             }
1190         }
1191         out.flush();
1192     }
1193
1194     public static SortedSet<String> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
1195         final SortedSet<String> all_domains_ids = new TreeSet<String>();
1196         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1197             final Set<String> all_domains = gwcd.getAllDomainIds();
1198             //    for( final Domain domain : all_domains ) {
1199             all_domains_ids.addAll( all_domains );
1200             //    }
1201         }
1202         return all_domains_ids;
1203     }
1204
1205     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
1206         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
1207         for( final Protein protein_domain_collection : protein_domain_collections ) {
1208             for( final Object name : protein_domain_collection.getProteinDomains() ) {
1209                 final BasicDomain protein_domain = ( BasicDomain ) name;
1210                 final String id = protein_domain.getDomainId();
1211                 if ( map.containsKey( id ) ) {
1212                     map.put( id, map.get( id ) + 1 );
1213                 }
1214                 else {
1215                     map.put( id, 1 );
1216                 }
1217             }
1218         }
1219         return map;
1220     }
1221
1222     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1223         final PhylogenyNodeIterator it = p.iteratorPostorder();
1224         int c = 0;
1225         while ( it.hasNext() ) {
1226             final PhylogenyNode n = it.next();
1227             if ( ForesterUtil.isEmpty( n.getName() )
1228                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1229                             .getScientificName() ) )
1230                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1231                             .getCommonName() ) ) ) {
1232                 if ( n.getParent() != null ) {
1233                     names.append( " " );
1234                     names.append( n.getParent().getName() );
1235                 }
1236                 final List l = n.getAllExternalDescendants();
1237                 for( final Object object : l ) {
1238                     System.out.println( l.toString() );
1239                 }
1240                 ++c;
1241             }
1242         }
1243         return c;
1244     }
1245
1246     public static void log( final String msg, final Writer w ) {
1247         try {
1248             w.write( msg );
1249             w.write( ForesterUtil.LINE_SEPARATOR );
1250         }
1251         catch ( final IOException e ) {
1252             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1253         }
1254     }
1255
1256     public static Phylogeny[] obtainAndPreProcessIntrees( final File[] intree_files,
1257                                                           final int number_of_genomes,
1258                                                           final String[][] input_file_properties ) {
1259         final Phylogeny[] intrees = new Phylogeny[ intree_files.length ];
1260         int i = 0;
1261         for( final File intree_file : intree_files ) {
1262             Phylogeny intree = null;
1263             final String error = ForesterUtil.isReadableFile( intree_file );
1264             if ( !ForesterUtil.isEmpty( error ) ) {
1265                 ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: "
1266                         + error );
1267             }
1268             try {
1269                 final Phylogeny[] p_array = ParserBasedPhylogenyFactory.getInstance()
1270                         .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
1271                 if ( p_array.length < 1 ) {
1272                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1273                             + "] does not contain any phylogeny in phyloXML format" );
1274                 }
1275                 else if ( p_array.length > 1 ) {
1276                     ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1277                             + "] contains more than one phylogeny in phyloXML format" );
1278                 }
1279                 intree = p_array[ 0 ];
1280             }
1281             catch ( final Exception e ) {
1282                 ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file
1283                         + "]: " + error );
1284             }
1285             if ( ( intree == null ) || intree.isEmpty() ) {
1286                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
1287             }
1288             if ( !intree.isRooted() ) {
1289                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
1290             }
1291             if ( intree.getNumberOfExternalNodes() < number_of_genomes ) {
1292                 ForesterUtil.fatalError( surfacing.PRG_NAME,
1293                                          "number of external nodes [" + intree.getNumberOfExternalNodes()
1294                                                  + "] of input tree [" + intree_file
1295                                                  + "] is smaller than the number of genomes the be analyzed ["
1296                                                  + number_of_genomes + "]" );
1297             }
1298             final StringBuilder parent_names = new StringBuilder();
1299             final int nodes_lacking_name = getNumberOfNodesLackingName( intree, parent_names );
1300             if ( nodes_lacking_name > 0 ) {
1301                 ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] has "
1302                         + nodes_lacking_name + " node(s) lacking a name [parent names:" + parent_names + "]" );
1303             }
1304             preparePhylogenyForParsimonyAnalyses( intree, input_file_properties );
1305             if ( !intree.isCompletelyBinary() ) {
1306                 ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "input tree [" + intree_file
1307                         + "] is not completely binary" );
1308             }
1309             intrees[ i++ ] = intree;
1310         }
1311         return intrees;
1312     }
1313
1314     public static Phylogeny obtainFirstIntree( final File intree_file ) {
1315         Phylogeny intree = null;
1316         final String error = ForesterUtil.isReadableFile( intree_file );
1317         if ( !ForesterUtil.isEmpty( error ) ) {
1318             ForesterUtil.fatalError( surfacing.PRG_NAME, "cannot read input tree file [" + intree_file + "]: " + error );
1319         }
1320         try {
1321             final Phylogeny[] phys = ParserBasedPhylogenyFactory.getInstance()
1322                     .create( intree_file, ParserUtils.createParserDependingOnFileType( intree_file, true ) );
1323             if ( phys.length < 1 ) {
1324                 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1325                         + "] does not contain any phylogeny in phyloXML format" );
1326             }
1327             else if ( phys.length > 1 ) {
1328                 ForesterUtil.fatalError( surfacing.PRG_NAME, "file [" + intree_file
1329                         + "] contains more than one phylogeny in phyloXML format" );
1330             }
1331             intree = phys[ 0 ];
1332         }
1333         catch ( final Exception e ) {
1334             ForesterUtil.fatalError( surfacing.PRG_NAME, "failed to read input tree from file [" + intree_file + "]: "
1335                     + error );
1336         }
1337         if ( ( intree == null ) || intree.isEmpty() ) {
1338             ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is empty" );
1339         }
1340         if ( !intree.isRooted() ) {
1341             ForesterUtil.fatalError( surfacing.PRG_NAME, "input tree [" + intree_file + "] is not rooted" );
1342         }
1343         return intree;
1344     }
1345
1346     public static String obtainHexColorStringDependingOnTaxonomyGroup( final String tax_code, final Phylogeny phy )
1347             throws IllegalArgumentException {
1348         if ( !_TAXCODE_HEXCOLORSTRING_MAP.containsKey( tax_code ) ) {
1349             if ( ( phy != null ) && !phy.isEmpty() ) {
1350                 final List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
1351                 Color c = null;
1352                 if ( ( nodes == null ) || nodes.isEmpty() ) {
1353                     throw new IllegalArgumentException( "code " + tax_code + " is not found" );
1354                 }
1355                 if ( nodes.size() != 1 ) {
1356                     throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
1357                 }
1358                 PhylogenyNode n = nodes.get( 0 );
1359                 while ( n != null ) {
1360                     if ( n.getNodeData().isHasTaxonomy()
1361                             && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
1362                         c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
1363                                 .getScientificName(), tax_code );
1364                     }
1365                     if ( ( c == null ) && !ForesterUtil.isEmpty( n.getName() ) ) {
1366                         c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName(), tax_code );
1367                     }
1368                     if ( c != null ) {
1369                         break;
1370                     }
1371                     n = n.getParent();
1372                 }
1373                 if ( c == null ) {
1374                     throw new IllegalArgumentException( "no color found for taxonomy code \"" + tax_code + "\"" );
1375                 }
1376                 final String hex = String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() );
1377                 _TAXCODE_HEXCOLORSTRING_MAP.put( tax_code, hex );
1378             }
1379             else {
1380                 throw new IllegalArgumentException( "unable to obtain color for code " + tax_code
1381                         + " (tree is null or empty and code is not in map)" );
1382             }
1383         }
1384         return _TAXCODE_HEXCOLORSTRING_MAP.get( tax_code );
1385     }
1386
1387
1388     public static String obtainTaxonomyGroup( final String tax_code, final Phylogeny phy )
1389             throws IllegalArgumentException {
1390         if ( !_TAXCODE_TAXGROUP_MAP.containsKey( tax_code ) ) {
1391             if ( ( phy != null ) && !phy.isEmpty() ) {
1392                 final List<PhylogenyNode> nodes = phy.getNodesViaTaxonomyCode( tax_code );
1393
1394                 if ( ( nodes == null ) || nodes.isEmpty() ) {
1395                     throw new IllegalArgumentException( "code " + tax_code + " is not found" );
1396                 }
1397                 if ( nodes.size() != 1 ) {
1398                     throw new IllegalArgumentException( "code " + tax_code + " is not unique" );
1399                 }
1400                 PhylogenyNode n = nodes.get( 0 );
1401                 String group = null;
1402                 Color c = null;
1403                 while ( n != null ) {
1404                     if ( n.getNodeData().isHasTaxonomy()
1405                             && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
1406                         c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getNodeData().getTaxonomy()
1407                                 .getScientificName(), tax_code );
1408
1409                         group = n.getNodeData().getTaxonomy()
1410                                 .getScientificName();
1411                     }
1412                     if ( ( c == null ) && !ForesterUtil.isEmpty( n.getName() ) ) {
1413                         c = ForesterUtil.obtainColorDependingOnTaxonomyGroup( n.getName(), tax_code );
1414                         group =  n.getName();
1415                     }
1416                     if ( c != null ) {
1417                         break;
1418                     }
1419                     group = null;
1420                     n = n.getParent();
1421                 }
1422                 if ( c == null ) {
1423                     throw new IllegalArgumentException( "no group found for taxonomy code \"" + tax_code + "\"" );
1424                 }
1425
1426                 _TAXCODE_TAXGROUP_MAP.put( tax_code, group );
1427             }
1428             else {
1429                 throw new IllegalArgumentException( "unable to obtain group for code " + tax_code
1430                         + " (tree is null or empty and code is not in map)" );
1431             }
1432         }
1433         return _TAXCODE_TAXGROUP_MAP.get( tax_code );
1434     }
1435
1436
1437
1438
1439     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
1440                                                           final SortedMap<String, Integer> domain_architecuture_counts,
1441                                                           final int min_count,
1442                                                           final File da_counts_outfile,
1443                                                           final File unique_da_outfile ) {
1444         checkForOutputFileWriteability( da_counts_outfile );
1445         checkForOutputFileWriteability( unique_da_outfile );
1446         try {
1447             final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
1448             final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
1449             final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
1450             while ( it.hasNext() ) {
1451                 final Map.Entry<String, Integer> e = it.next();
1452                 final String da = e.getKey();
1453                 final int count = e.getValue();
1454                 if ( count >= min_count ) {
1455                     da_counts_out.write( da );
1456                     da_counts_out.write( "\t" );
1457                     da_counts_out.write( String.valueOf( count ) );
1458                     da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
1459                 }
1460                 if ( count == 1 ) {
1461                     final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
1462                     while ( it2.hasNext() ) {
1463                         final Map.Entry<String, Set<String>> e2 = it2.next();
1464                         final String genome = e2.getKey();
1465                         final Set<String> das = e2.getValue();
1466                         if ( das.contains( da ) ) {
1467                             unique_da_out.write( genome );
1468                             unique_da_out.write( "\t" );
1469                             unique_da_out.write( da );
1470                             unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
1471                         }
1472                     }
1473                 }
1474             }
1475             unique_da_out.close();
1476             da_counts_out.close();
1477         }
1478         catch ( final IOException e ) {
1479             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1480         }
1481         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
1482         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
1483         //
1484     }
1485
1486     public static void preparePhylogeny( final Phylogeny p,
1487                                          final DomainParsimonyCalculator domain_parsimony,
1488                                          final String date_time,
1489                                          final String method,
1490                                          final String name,
1491                                          final String parameters_str ) {
1492         domain_parsimony.decoratePhylogenyWithDomains( p );
1493         final StringBuilder desc = new StringBuilder();
1494         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1495         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1496         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1497         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1498         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1499         desc.append( "[Parameters: " + parameters_str + "]" );
1500         p.setName( name );
1501         p.setDescription( desc.toString() );
1502         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1503         p.setRerootable( false );
1504         p.setRooted( true );
1505     }
1506
1507     public static void preparePhylogenyForParsimonyAnalyses( final Phylogeny intree,
1508                                                              final String[][] input_file_properties ) {
1509         final String[] genomes = new String[ input_file_properties.length ];
1510         for( int i = 0; i < input_file_properties.length; ++i ) {
1511             if ( intree.getNodes( input_file_properties[ i ][ 1 ] ).size() > 1 ) {
1512                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_properties[ i ][ 1 ]
1513                         + "] is not unique in input tree " + intree.getName() );
1514             }
1515             genomes[ i ] = input_file_properties[ i ][ 1 ];
1516         }
1517         //
1518         final PhylogenyNodeIterator it = intree.iteratorPostorder();
1519         while ( it.hasNext() ) {
1520             final PhylogenyNode n = it.next();
1521             if ( ForesterUtil.isEmpty( n.getName() ) ) {
1522                 if ( n.getNodeData().isHasTaxonomy()
1523                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getTaxonomyCode() ) ) {
1524                     n.setName( n.getNodeData().getTaxonomy().getTaxonomyCode() );
1525                 }
1526                 else if ( n.getNodeData().isHasTaxonomy()
1527                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getScientificName() ) ) {
1528                     n.setName( n.getNodeData().getTaxonomy().getScientificName() );
1529                 }
1530                 else if ( n.getNodeData().isHasTaxonomy()
1531                         && !ForesterUtil.isEmpty( n.getNodeData().getTaxonomy().getCommonName() ) ) {
1532                     n.setName( n.getNodeData().getTaxonomy().getCommonName() );
1533                 }
1534                 else {
1535                     ForesterUtil
1536                             .fatalError( surfacing.PRG_NAME,
1537                                          "node with no name, scientific name, common name, or taxonomy code present" );
1538                 }
1539             }
1540         }
1541         //
1542         final List<String> igns = PhylogenyMethods.deleteExternalNodesPositiveSelection( genomes, intree );
1543         if ( igns.size() > 0 ) {
1544             System.out.println( "Not using the following " + igns.size() + " nodes:" );
1545             for( int i = 0; i < igns.size(); ++i ) {
1546                 System.out.println( " " + i + ": " + igns.get( i ) );
1547             }
1548             System.out.println( "--" );
1549         }
1550         for( final String[] input_file_propertie : input_file_properties ) {
1551             try {
1552                 intree.getNode( input_file_propertie[ 1 ] );
1553             }
1554             catch ( final IllegalArgumentException e ) {
1555                 ForesterUtil.fatalError( surfacing.PRG_NAME, "node named [" + input_file_propertie[ 1 ]
1556                         + "] not present/not unique in input tree" );
1557             }
1558         }
1559     }
1560
1561     public static void printOutPercentageOfMultidomainProteins( final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
1562                                                                 final Writer log_writer ) {
1563         int sum = 0;
1564         for( final Entry<Integer, Integer> entry : all_genomes_domains_per_potein_histo.entrySet() ) {
1565             sum += entry.getValue();
1566         }
1567         final double percentage = ( 100.0 * ( sum - all_genomes_domains_per_potein_histo.get( 1 ) ) ) / sum;
1568         ForesterUtil.programMessage( surfacing.PRG_NAME, "Percentage of multidomain proteins: " + percentage + "%" );
1569         log( "Percentage of multidomain proteins:            : " + percentage + "%", log_writer );
1570     }
1571
1572     public static void processFilter( final File filter_file, final SortedSet<String> filter ) {
1573         SortedSet<String> filter_str = null;
1574         try {
1575             filter_str = ForesterUtil.file2set( filter_file );
1576         }
1577         catch ( final IOException e ) {
1578             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1579         }
1580         if ( filter_str != null ) {
1581             for( final String string : filter_str ) {
1582                 filter.add( string );
1583             }
1584         }
1585         if ( surfacing.VERBOSE ) {
1586             System.out.println( "Filter:" );
1587             for( final String domainId : filter ) {
1588                 System.out.println( domainId );
1589             }
1590         }
1591     }
1592
1593     public static String[][] processInputGenomesFile( final File input_genomes ) {
1594         String[][] input_file_properties = null;
1595         try {
1596             input_file_properties = ForesterUtil.file22dArray( input_genomes );
1597         }
1598         catch ( final IOException e ) {
1599             ForesterUtil.fatalError( surfacing.PRG_NAME,
1600                                      "genomes files is to be in the following format \"<hmmpfam output file> <species>\": "
1601                                              + e.getLocalizedMessage() );
1602         }
1603         final Set<String> specs = new HashSet<String>();
1604         final Set<String> paths = new HashSet<String>();
1605         for( int i = 0; i < input_file_properties.length; ++i ) {
1606             if ( !PhyloXmlUtil.TAXOMONY_CODE_PATTERN.matcher( input_file_properties[ i ][ 1 ] ).matches() ) {
1607                 ForesterUtil.fatalError( surfacing.PRG_NAME, "illegal format for species code: "
1608                         + input_file_properties[ i ][ 1 ] );
1609             }
1610             if ( specs.contains( input_file_properties[ i ][ 1 ] ) ) {
1611                 ForesterUtil.fatalError( surfacing.PRG_NAME, "species code " + input_file_properties[ i ][ 1 ]
1612                         + " is not unique" );
1613             }
1614             specs.add( input_file_properties[ i ][ 1 ] );
1615             if ( paths.contains( input_file_properties[ i ][ 0 ] ) ) {
1616                 ForesterUtil.fatalError( surfacing.PRG_NAME, "path " + input_file_properties[ i ][ 0 ]
1617                         + " is not unique" );
1618             }
1619             paths.add( input_file_properties[ i ][ 0 ] );
1620             final String error = ForesterUtil.isReadableFile( new File( input_file_properties[ i ][ 0 ] ) );
1621             if ( !ForesterUtil.isEmpty( error ) ) {
1622                 ForesterUtil.fatalError( surfacing.PRG_NAME, error );
1623             }
1624         }
1625         return input_file_properties;
1626     }
1627
1628     public static void processPlusMinusAnalysisOption( final CommandLineArguments cla,
1629                                                        final List<String> high_copy_base,
1630                                                        final List<String> high_copy_target,
1631                                                        final List<String> low_copy,
1632                                                        final List<Object> numbers ) {
1633         if ( cla.isOptionSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
1634             if ( !cla.isOptionValueSet( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) ) {
1635                 ForesterUtil.fatalError( surfacing.PRG_NAME, "no value for 'plus-minus' file: -"
1636                         + surfacing.PLUS_MINUS_ANALYSIS_OPTION + "=<file>" );
1637             }
1638             final File plus_minus_file = new File( cla.getOptionValue( surfacing.PLUS_MINUS_ANALYSIS_OPTION ) );
1639             final String msg = ForesterUtil.isReadableFile( plus_minus_file );
1640             if ( !ForesterUtil.isEmpty( msg ) ) {
1641                 ForesterUtil.fatalError( surfacing.PRG_NAME, "can not read from \"" + plus_minus_file + "\": " + msg );
1642             }
1643             processPlusMinusFile( plus_minus_file, high_copy_base, high_copy_target, low_copy, numbers );
1644         }
1645     }
1646
1647     // First numbers is minimal difference, second is factor.
1648     public static void processPlusMinusFile( final File plus_minus_file,
1649                                              final List<String> high_copy_base,
1650                                              final List<String> high_copy_target,
1651                                              final List<String> low_copy,
1652                                              final List<Object> numbers ) {
1653         Set<String> species_set = null;
1654         int min_diff = surfacing.PLUS_MINUS_ANALYSIS_MIN_DIFF_DEFAULT;
1655         double factor = surfacing.PLUS_MINUS_ANALYSIS_FACTOR_DEFAULT;
1656         try {
1657             species_set = ForesterUtil.file2set( plus_minus_file );
1658         }
1659         catch ( final IOException e ) {
1660             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1661         }
1662         if ( species_set != null ) {
1663             for( final String species : species_set ) {
1664                 final String species_trimmed = species.substring( 1 );
1665                 if ( species.startsWith( "+" ) ) {
1666                     if ( low_copy.contains( species_trimmed ) ) {
1667                         ForesterUtil.fatalError( surfacing.PRG_NAME,
1668                                                  "species/genome names can not appear with both '+' and '-' suffix, as appears the case for: \""
1669                                                          + species_trimmed + "\"" );
1670                     }
1671                     high_copy_base.add( species_trimmed );
1672                 }
1673                 else if ( species.startsWith( "*" ) ) {
1674                     if ( low_copy.contains( species_trimmed ) ) {
1675                         ForesterUtil.fatalError( surfacing.PRG_NAME,
1676                                                  "species/genome names can not appear with both '*' and '-' suffix, as appears the case for: \""
1677                                                          + species_trimmed + "\"" );
1678                     }
1679                     high_copy_target.add( species_trimmed );
1680                 }
1681                 else if ( species.startsWith( "-" ) ) {
1682                     if ( high_copy_base.contains( species_trimmed ) || high_copy_target.contains( species_trimmed ) ) {
1683                         ForesterUtil.fatalError( surfacing.PRG_NAME,
1684                                                  "species/genome names can not appear with both '+' or '*' and '-' suffix, as appears the case for: \""
1685                                                          + species_trimmed + "\"" );
1686                     }
1687                     low_copy.add( species_trimmed );
1688                 }
1689                 else if ( species.startsWith( "$D" ) ) {
1690                     try {
1691                         min_diff = Integer.parseInt( species.substring( 3 ) );
1692                     }
1693                     catch ( final NumberFormatException e ) {
1694                         ForesterUtil.fatalError( surfacing.PRG_NAME,
1695                                                  "could not parse integer value for minimal difference from: \""
1696                                                          + species.substring( 3 ) + "\"" );
1697                     }
1698                 }
1699                 else if ( species.startsWith( "$F" ) ) {
1700                     try {
1701                         factor = Double.parseDouble( species.substring( 3 ) );
1702                     }
1703                     catch ( final NumberFormatException e ) {
1704                         ForesterUtil.fatalError( surfacing.PRG_NAME, "could not parse double value for factor from: \""
1705                                 + species.substring( 3 ) + "\"" );
1706                     }
1707                 }
1708                 else if ( species.startsWith( "#" ) ) {
1709                     // Comment, ignore.
1710                 }
1711                 else {
1712                     ForesterUtil
1713                             .fatalError( surfacing.PRG_NAME,
1714                                          "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: \""
1715                                                  + species + "\"" );
1716                 }
1717                 numbers.add( new Integer( min_diff + "" ) );
1718                 numbers.add( new Double( factor + "" ) );
1719             }
1720         }
1721         else {
1722             ForesterUtil.fatalError( surfacing.PRG_NAME, "'plus minus' file [" + plus_minus_file + "] appears empty" );
1723         }
1724     }
1725
1726     /*
1727      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1728      *
1729      *
1730      */
1731     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1732                                                             final String protein_id,
1733                                                             final String separator ) {
1734         final StringBuffer sb = new StringBuffer();
1735         if ( protein.getSpecies() == null ) {
1736             throw new IllegalArgumentException( "species must not be null" );
1737         }
1738         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1739             throw new IllegalArgumentException( "species id must not be empty" );
1740         }
1741         final List<Domain> domains = protein.getProteinDomains();
1742         if ( domains.size() > 1 ) {
1743             final Map<String, Integer> counts = new HashMap<String, Integer>();
1744             for( final Domain domain : domains ) {
1745                 final String id = domain.getDomainId();
1746                 if ( counts.containsKey( id ) ) {
1747                     counts.put( id, counts.get( id ) + 1 );
1748                 }
1749                 else {
1750                     counts.put( id, 1 );
1751                 }
1752             }
1753             final Set<String> dcs = new HashSet<String>();
1754             for( int i = 1; i < domains.size(); ++i ) {
1755                 for( int j = 0; j < i; ++j ) {
1756                     Domain domain_n = domains.get( i );
1757                     Domain domain_c = domains.get( j );
1758                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1759                         domain_n = domains.get( j );
1760                         domain_c = domains.get( i );
1761                     }
1762                     final String dc = domain_n.getDomainId() + domain_c.getDomainId();
1763                     if ( !dcs.contains( dc ) ) {
1764                         dcs.add( dc );
1765                         sb.append( protein.getSpecies() );
1766                         sb.append( separator );
1767                         sb.append( protein_id );
1768                         sb.append( separator );
1769                         sb.append( domain_n.getDomainId() );
1770                         sb.append( separator );
1771                         sb.append( domain_c.getDomainId() );
1772                         sb.append( separator );
1773                         sb.append( domain_n.getPerDomainEvalue() );
1774                         sb.append( separator );
1775                         sb.append( domain_c.getPerDomainEvalue() );
1776                         sb.append( separator );
1777                         sb.append( counts.get( domain_n.getDomainId() ) );
1778                         sb.append( separator );
1779                         sb.append( counts.get( domain_c.getDomainId() ) );
1780                         sb.append( ForesterUtil.LINE_SEPARATOR );
1781                     }
1782                 }
1783             }
1784         }
1785         else if ( domains.size() == 1 ) {
1786             sb.append( protein.getSpecies() );
1787             sb.append( separator );
1788             sb.append( protein_id );
1789             sb.append( separator );
1790             sb.append( domains.get( 0 ).getDomainId() );
1791             sb.append( separator );
1792             sb.append( separator );
1793             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1794             sb.append( separator );
1795             sb.append( separator );
1796             sb.append( 1 );
1797             sb.append( separator );
1798             sb.append( ForesterUtil.LINE_SEPARATOR );
1799         }
1800         else {
1801             sb.append( protein.getSpecies() );
1802             sb.append( separator );
1803             sb.append( protein_id );
1804             sb.append( separator );
1805             sb.append( separator );
1806             sb.append( separator );
1807             sb.append( separator );
1808             sb.append( separator );
1809             sb.append( separator );
1810             sb.append( ForesterUtil.LINE_SEPARATOR );
1811         }
1812         return sb;
1813     }
1814
1815     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1816         final List<Domain> domains = new ArrayList<Domain>();
1817         for( final Domain d : protein.getProteinDomains() ) {
1818             domains.add( d );
1819         }
1820         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1821         return domains;
1822     }
1823
1824     public static int storeDomainArchitectures( final String genome,
1825                                                 final SortedMap<String, Set<String>> domain_architecutures,
1826                                                 final List<Protein> protein_list,
1827                                                 final Map<String, Integer> distinct_domain_architecuture_counts ) {
1828         final Set<String> da = new HashSet<String>();
1829         domain_architecutures.put( genome, da );
1830         for( final Protein protein : protein_list ) {
1831             final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
1832             if ( !da.contains( da_str ) ) {
1833                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
1834                     distinct_domain_architecuture_counts.put( da_str, 1 );
1835                 }
1836                 else {
1837                     distinct_domain_architecuture_counts.put( da_str,
1838                                                               distinct_domain_architecuture_counts.get( da_str ) + 1 );
1839                 }
1840                 da.add( da_str );
1841             }
1842         }
1843         return da.size();
1844     }
1845
1846     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1847                                                             final boolean get_gains,
1848                                                             final String outdir,
1849                                                             final String suffix_for_filename ) throws IOException {
1850         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1851         if ( !get_gains ) {
1852             state = CharacterStateMatrix.GainLossStates.LOSS;
1853         }
1854         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1855                                                                   false,
1856                                                                   state,
1857                                                                   outdir );
1858         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1859             final PhylogenyNode node = it.next();
1860             if ( !node.isExternal() ) {
1861                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1862                 if ( domains.size() > 0 ) {
1863                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1864                             + node.getName() + suffix_for_filename );
1865                     for( final String domain : domains ) {
1866                         writer.write( domain );
1867                         writer.write( ForesterUtil.LINE_SEPARATOR );
1868                     }
1869                     writer.close();
1870                 }
1871             }
1872         }
1873     }
1874
1875     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1876                                                                           final File output_dir,
1877                                                                           final GenomeWideCombinableDomains gwcd,
1878                                                                           final int i,
1879                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1880         File dc_outfile_dot = new File( input_file_properties[ i ][ 1 ]
1881                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1882         if ( output_dir != null ) {
1883             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1884         }
1885         checkForOutputFileWriteability( dc_outfile_dot );
1886         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1887         try {
1888             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1889             for( final BinaryDomainCombination bdc : binary_combinations ) {
1890                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1891                         .toString() );
1892                 out_dot.write( SurfacingConstants.NL );
1893             }
1894             out_dot.close();
1895         }
1896         catch ( final IOException e ) {
1897             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1898         }
1899         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1900                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1901                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1902     }
1903
1904     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1905                                                             final CharacterStateMatrix.GainLossStates state,
1906                                                             final String filename,
1907                                                             final String indentifier_characters_separator,
1908                                                             final String character_separator,
1909                                                             final Map<String, String> descriptions ) {
1910         final File outfile = new File( filename );
1911         checkForOutputFileWriteability( outfile );
1912         final SortedSet<String> sorted_ids = new TreeSet<String>();
1913         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1914             sorted_ids.add( matrix.getIdentifier( i ) );
1915         }
1916         try {
1917             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1918             for( final String id : sorted_ids ) {
1919                 out.write( indentifier_characters_separator );
1920                 out.write( "#" + id );
1921                 out.write( indentifier_characters_separator );
1922                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1923                     // Not nice:
1924                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1925                     if ( ( matrix.getState( id, c ) == state )
1926                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1927                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1928                         out.write( matrix.getCharacter( c ) );
1929                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1930                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1931                             out.write( "\t" );
1932                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1933                         }
1934                         out.write( character_separator );
1935                     }
1936                 }
1937             }
1938             out.flush();
1939             out.close();
1940         }
1941         catch ( final IOException e ) {
1942             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1943         }
1944         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1945     }
1946
1947     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1948                                                                                                  final CharacterStateMatrix.GainLossStates state,
1949                                                                                                  final String filename,
1950                                                                                                  final String indentifier_characters_separator,
1951                                                                                                  final String character_separator,
1952                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1953         final File outfile = new File( filename );
1954         checkForOutputFileWriteability( outfile );
1955         final SortedSet<String> sorted_ids = new TreeSet<String>();
1956         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1957             sorted_ids.add( matrix.getIdentifier( i ) );
1958         }
1959         try {
1960             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1961             for( final String id : sorted_ids ) {
1962                 out.write( indentifier_characters_separator );
1963                 out.write( "#" + id );
1964                 out.write( indentifier_characters_separator );
1965                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1966                     // Not nice:
1967                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1968                     if ( ( matrix.getState( id, c ) == state )
1969                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1970                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1971                         BinaryDomainCombination bdc = null;
1972                         try {
1973                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1974                         }
1975                         catch ( final Exception e ) {
1976                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1977                         }
1978                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1979                         out.write( character_separator );
1980                     }
1981                 }
1982             }
1983             out.flush();
1984             out.close();
1985         }
1986         catch ( final IOException e ) {
1987             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1988         }
1989         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1990     }
1991
1992     public static void writeBinaryStatesMatrixToList( final Map<String, List<GoId>> domain_id_to_go_ids_map,
1993                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1994                                                       final GoNameSpace go_namespace_limit,
1995                                                       final boolean domain_combinations,
1996                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1997                                                       final CharacterStateMatrix.GainLossStates state,
1998                                                       final String filename,
1999                                                       final String indentifier_characters_separator,
2000                                                       final String character_separator,
2001                                                       final String title_for_html,
2002                                                       final String prefix_for_html,
2003                                                       final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
2004                                                       final SortedSet<String> all_pfams_encountered,
2005                                                       final SortedSet<String> pfams_gained_or_lost,
2006                                                       final String suffix_for_per_node_events_file,
2007                                                       final Map<String, Integer> tax_code_to_id_map ) {
2008         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
2009             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
2010         }
2011         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
2012             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
2013         }
2014         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
2015             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
2016         }
2017         final File outfile = new File( filename );
2018         checkForOutputFileWriteability( outfile );
2019         final SortedSet<String> sorted_ids = new TreeSet<String>();
2020         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
2021             sorted_ids.add( matrix.getIdentifier( i ) );
2022         }
2023         try {
2024             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
2025             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
2026                                                                                                                 domain_combinations,
2027                                                                                                                 state,
2028                                                                                                                 filename );
2029             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
2030             File per_node_go_mapped_domain_gain_loss_outfile = null;
2031             int per_node_counter = 0;
2032             out.write( "<html>" );
2033             out.write( SurfacingConstants.NL );
2034             writeHtmlHead( out, title_for_html );
2035             out.write( SurfacingConstants.NL );
2036             out.write( "<body>" );
2037             out.write( SurfacingConstants.NL );
2038             out.write( "<h1>" );
2039             out.write( SurfacingConstants.NL );
2040             out.write( title_for_html );
2041             out.write( SurfacingConstants.NL );
2042             out.write( "</h1>" );
2043             out.write( SurfacingConstants.NL );
2044             out.write( "<table>" );
2045             out.write( SurfacingConstants.NL );
2046             for( final String id : sorted_ids ) {
2047                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
2048                 if ( matcher.matches() ) {
2049                     continue;
2050                 }
2051                 out.write( "<tr>" );
2052                 out.write( "<td>" );
2053                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
2054                 out.write( "</td>" );
2055                 out.write( "</tr>" );
2056                 out.write( SurfacingConstants.NL );
2057             }
2058             out.write( "</table>" );
2059             out.write( SurfacingConstants.NL );
2060             for( final String id : sorted_ids ) {
2061                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
2062                 if ( matcher.matches() ) {
2063                     continue;
2064                 }
2065                 out.write( SurfacingConstants.NL );
2066                 out.write( "<h2>" );
2067                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
2068                 writeTaxonomyLinks( out, id, tax_code_to_id_map );
2069                 out.write( "</h2>" );
2070                 out.write( SurfacingConstants.NL );
2071                 out.write( "<table>" );
2072                 out.write( SurfacingConstants.NL );
2073                 out.write( "<tr>" );
2074                 out.write( "<td><b>" );
2075                 out.write( "Pfam domain(s)" );
2076                 out.write( "</b></td><td><b>" );
2077                 out.write( "GO term acc" );
2078                 out.write( "</b></td><td><b>" );
2079                 out.write( "GO term" );
2080                 out.write( "</b></td><td><b>" );
2081                 out.write( "GO namespace" );
2082                 out.write( "</b></td>" );
2083                 out.write( "</tr>" );
2084                 out.write( SurfacingConstants.NL );
2085                 out.write( "</tr>" );
2086                 out.write( SurfacingConstants.NL );
2087                 per_node_counter = 0;
2088                 if ( matrix.getNumberOfCharacters() > 0 ) {
2089                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2090                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
2091                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
2092                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
2093                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
2094                 }
2095                 else {
2096                     per_node_go_mapped_domain_gain_loss_outfile = null;
2097                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
2098                 }
2099                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
2100                     // Not nice:
2101                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
2102                     if ( ( matrix.getState( id, c ) == state )
2103                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
2104                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
2105                         final String character = matrix.getCharacter( c );
2106                         String domain_0 = "";
2107                         String domain_1 = "";
2108                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
2109                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
2110                             if ( s.length != 2 ) {
2111                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
2112                                         + character + "]" );
2113                             }
2114                             domain_0 = s[ 0 ];
2115                             domain_1 = s[ 1 ];
2116                         }
2117                         else {
2118                             domain_0 = character;
2119                         }
2120                         writeDomainData( domain_id_to_go_ids_map,
2121                                          go_id_to_term_map,
2122                                          go_namespace_limit,
2123                                          out,
2124                                          domain_0,
2125                                          domain_1,
2126                                          prefix_for_html,
2127                                          character_separator,
2128                                          domain_id_to_secondary_features_maps,
2129                                          null );
2130                         all_pfams_encountered.add( domain_0 );
2131                         if ( pfams_gained_or_lost != null ) {
2132                             pfams_gained_or_lost.add( domain_0 );
2133                         }
2134                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2135                             all_pfams_encountered.add( domain_1 );
2136                             if ( pfams_gained_or_lost != null ) {
2137                                 pfams_gained_or_lost.add( domain_1 );
2138                             }
2139                         }
2140                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
2141                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
2142                                                                      domain_0,
2143                                                                      domain_1 );
2144                             per_node_counter++;
2145                         }
2146                     }
2147                 }
2148                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
2149                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
2150                     if ( per_node_counter < 1 ) {
2151                         per_node_go_mapped_domain_gain_loss_outfile.delete();
2152                     }
2153                     per_node_counter = 0;
2154                 }
2155                 out.write( "</table>" );
2156                 out.write( SurfacingConstants.NL );
2157                 out.write( "<hr>" );
2158                 out.write( SurfacingConstants.NL );
2159             } // for( final String id : sorted_ids ) {
2160             out.write( "</body>" );
2161             out.write( SurfacingConstants.NL );
2162             out.write( "</html>" );
2163             out.write( SurfacingConstants.NL );
2164             out.flush();
2165             out.close();
2166         }
2167         catch ( final IOException e ) {
2168             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2169         }
2170         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
2171     }
2172
2173     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
2174                                                           final File output_dir,
2175                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
2176                                                           final GenomeWideCombinableDomains gwcd,
2177                                                           final int i,
2178                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
2179         File dc_outfile = new File( input_file_properties[ i ][ 1 ]
2180                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
2181         if ( output_dir != null ) {
2182             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
2183         }
2184         checkForOutputFileWriteability( dc_outfile );
2185         try {
2186             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
2187             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
2188             out.close();
2189         }
2190         catch ( final IOException e ) {
2191             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2192         }
2193         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
2194         try {
2195             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 1 ] + "\t" );
2196             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
2197             if ( stats.getN() < 2 ) {
2198                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
2199             }
2200             else {
2201                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
2202                         .sampleStandardDeviation() ) + "\t" );
2203             }
2204             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
2205             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
2206             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
2207             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
2208             final SortedSet<String> mpds = gwcd.getMostPromiscuosDomain();
2209             for( final String mpd : mpds ) {
2210                 per_genome_domain_promiscuity_statistics_writer.write( mpd + " " );
2211             }
2212             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
2213         }
2214         catch ( final IOException e ) {
2215             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2216         }
2217         if ( input_file_properties[ i ].length == 3 ) {
2218             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2219                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
2220                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
2221         }
2222         else {
2223             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2224                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
2225                     + dc_outfile + "\"" );
2226         }
2227     }
2228
2229     public static void writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2230                                                       final StringBuilder html_title,
2231                                                       final Writer simple_tab_writer,
2232                                                       final Writer single_writer,
2233                                                       Map<Character, Writer> split_writers,
2234                                                       final SortedSet<DomainSimilarity> similarities,
2235                                                       final boolean treat_as_binary,
2236                                                       final List<Species> species_order,
2237                                                       final PrintableDomainSimilarity.PRINT_OPTION print_option,
2238                                                       final DomainSimilarity.DomainSimilarityScoring scoring,
2239                                                       final boolean verbose,
2240                                                       final Map<String, Integer> tax_code_to_id_map,
2241                                                       final Phylogeny phy ) throws IOException {
2242         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
2243             split_writers = new HashMap<Character, Writer>();
2244             split_writers.put( '_', single_writer );
2245         }
2246         switch ( print_option ) {
2247             case SIMPLE_TAB_DELIMITED:
2248                 break;
2249             case HTML:
2250                 for( final Character key : split_writers.keySet() ) {
2251                     final Writer w = split_writers.get( key );
2252                     w.write( "<html>" );
2253                     w.write( SurfacingConstants.NL );
2254                     if ( key != '_' ) {
2255                         writeHtmlHead( w, "DC analysis (" + html_title + ") " + key.toString().toUpperCase() );
2256                     }
2257                     else {
2258                         writeHtmlHead( w, "DC analysis (" + html_title + ")" );
2259                     }
2260                     w.write( SurfacingConstants.NL );
2261                     w.write( "<body>" );
2262                     w.write( SurfacingConstants.NL );
2263                     w.write( html_desc.toString() );
2264                     w.write( SurfacingConstants.NL );
2265                     w.write( "<hr>" );
2266                     w.write( SurfacingConstants.NL );
2267                     w.write( "<br>" );
2268                     w.write( SurfacingConstants.NL );
2269                     w.write( "<table>" );
2270                     w.write( SurfacingConstants.NL );
2271                     w.write( "<tr><td><b>Domains:</b></td></tr>" );
2272                     w.write( SurfacingConstants.NL );
2273                 }
2274                 break;
2275         }
2276         //
2277         for( final DomainSimilarity similarity : similarities ) {
2278             if ( ( species_order != null ) && !species_order.isEmpty() ) {
2279                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2280             }
2281             if ( single_writer != null ) {
2282                 single_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
2283                         + similarity.getDomainId() + "</a></b></td></tr>" );
2284                 single_writer.write( SurfacingConstants.NL );
2285             }
2286             else {
2287                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
2288                         .charAt( 0 ) );
2289                 if ( local_writer == null ) {
2290                     local_writer = split_writers.get( '0' );
2291                 }
2292                 local_writer.write( "<tr><td><b><a href=\"#" + similarity.getDomainId() + "\">"
2293                         + similarity.getDomainId() + "</a></b></td></tr>" );
2294                 local_writer.write( SurfacingConstants.NL );
2295             }
2296         }
2297         for( final Writer w : split_writers.values() ) {
2298             w.write( "</table>" );
2299             w.write( SurfacingConstants.NL );
2300             w.write( "<hr>" );
2301             w.write( SurfacingConstants.NL );
2302             //
2303             w.write( "<table>" );
2304             w.write( SurfacingConstants.NL );
2305             w.write( "<tr><td><b>" );
2306             w.write( "Species group colors:" );
2307             w.write( "</b></td></tr>" );
2308             w.write( SurfacingConstants.NL );
2309             writeColorLabels( "Deuterostomia", TaxonomyColors.DEUTEROSTOMIA_COLOR, w );
2310             writeColorLabels( "Protostomia", TaxonomyColors.PROTOSTOMIA_COLOR, w );
2311             writeColorLabels( "Cnidaria", TaxonomyColors.CNIDARIA_COLOR, w );
2312             writeColorLabels( "Placozoa", TaxonomyColors.PLACOZOA_COLOR, w );
2313             writeColorLabels( "Ctenophora (comb jellies)", TaxonomyColors.CTENOPHORA_COLOR, w );
2314             writeColorLabels( "Porifera (sponges)", TaxonomyColors.PORIFERA_COLOR, w );
2315             writeColorLabels( "Choanoflagellida", TaxonomyColors.CHOANOFLAGELLIDA, w );
2316             writeColorLabels( "Ichthyosporea & Filasterea", TaxonomyColors.ICHTHYOSPOREA_AND_FILASTEREA, w );
2317             writeColorLabels( "Dikarya (Ascomycota & Basidiomycota, so-called \"higher fungi\")",
2318                               TaxonomyColors.DIKARYA_COLOR,
2319                               w );
2320             writeColorLabels( "other Fungi", TaxonomyColors.OTHER_FUNGI_COLOR, w );
2321             writeColorLabels( "Nucleariidae and Fonticula group",
2322                               TaxonomyColors.NUCLEARIIDAE_AND_FONTICULA_GROUP_COLOR,
2323                               w );
2324             writeColorLabels( "Amoebozoa", TaxonomyColors.AMOEBOZOA_COLOR, w );
2325             writeColorLabels( "Embryophyta (plants)", TaxonomyColors.EMBRYOPHYTA_COLOR, w );
2326             writeColorLabels( "Chlorophyta (green algae)", TaxonomyColors.CHLOROPHYTA_COLOR, w );
2327             writeColorLabels( "Rhodophyta (red algae)", TaxonomyColors.RHODOPHYTA_COLOR, w );
2328             writeColorLabels( "Glaucocystophyce (Glaucophyta)", TaxonomyColors.GLAUCOPHYTA_COLOR, w );
2329             writeColorLabels( "Hacrobia (Cryptophyta & Haptophyceae & Centroheliozoa)",
2330                               TaxonomyColors.HACROBIA_COLOR,
2331                               w );
2332             writeColorLabels( "Stramenopiles (Chromophyta, heterokonts)", TaxonomyColors.STRAMENOPILES_COLOR, w );
2333             writeColorLabels( "Alveolata", TaxonomyColors.ALVEOLATA_COLOR, w );
2334             writeColorLabels( "Rhizaria", TaxonomyColors.RHIZARIA_COLOR, w );
2335             writeColorLabels( "Excavata", TaxonomyColors.EXCAVATA_COLOR, w );
2336             writeColorLabels( "Apusozoa", TaxonomyColors.APUSOZOA_COLOR, w );
2337             writeColorLabels( "Archaea", TaxonomyColors.ARCHAEA_COLOR, w );
2338             writeColorLabels( "Bacteria", TaxonomyColors.BACTERIA_COLOR, w );
2339             w.write( "</table>" );
2340             w.write( SurfacingConstants.NL );
2341             //
2342             w.write( "<hr>" );
2343             w.write( SurfacingConstants.NL );
2344             w.write( "<table>" );
2345             w.write( SurfacingConstants.NL );
2346         }
2347         //
2348         for( final DomainSimilarity similarity : similarities ) {
2349             if ( ( species_order != null ) && !species_order.isEmpty() ) {
2350                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2351             }
2352             if ( simple_tab_writer != null ) {
2353                 simple_tab_writer.write( similarity.toStringBuffer( PRINT_OPTION.SIMPLE_TAB_DELIMITED,
2354                                                                     tax_code_to_id_map,
2355                                                                     null ).toString() );
2356             }
2357             if ( single_writer != null ) {
2358                 single_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
2359                 single_writer.write( SurfacingConstants.NL );
2360             }
2361             else {
2362                 Writer local_writer = split_writers.get( ( similarity.getDomainId().charAt( 0 ) + "" ).toLowerCase()
2363                         .charAt( 0 ) );
2364                 if ( local_writer == null ) {
2365                     local_writer = split_writers.get( '0' );
2366                 }
2367                 local_writer.write( similarity.toStringBuffer( print_option, tax_code_to_id_map, phy ).toString() );
2368                 local_writer.write( SurfacingConstants.NL );
2369             }
2370         }
2371         switch ( print_option ) {
2372             case HTML:
2373                 for( final Writer w : split_writers.values() ) {
2374                     w.write( SurfacingConstants.NL );
2375                     w.write( "</table>" );
2376                     w.write( SurfacingConstants.NL );
2377                     w.write( "</font>" );
2378                     w.write( SurfacingConstants.NL );
2379                     w.write( "</body>" );
2380                     w.write( SurfacingConstants.NL );
2381                     w.write( "</html>" );
2382                     w.write( SurfacingConstants.NL );
2383                 }
2384                 break;
2385             default:
2386                 break;
2387         }
2388         for( final Writer w : split_writers.values() ) {
2389             w.close();
2390         }
2391     }
2392
2393     public static void writeHtmlHead( final Writer w, final String title ) throws IOException {
2394         w.write( SurfacingConstants.NL );
2395         w.write( "<head>" );
2396         w.write( "<title>" );
2397         w.write( title );
2398         w.write( "</title>" );
2399         w.write( SurfacingConstants.NL );
2400         w.write( "<style>" );
2401         w.write( SurfacingConstants.NL );
2402         w.write( "a:visited { color : #000066; text-decoration : none; }" );
2403         w.write( SurfacingConstants.NL );
2404         w.write( "a:link { color : #000066; text-decoration : none; }" );
2405         w.write( SurfacingConstants.NL );
2406         w.write( "a:active { color : ##000066; text-decoration : none; }" );
2407         w.write( SurfacingConstants.NL );
2408         w.write( "a:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; }" );
2409         w.write( SurfacingConstants.NL );
2410         //
2411         w.write( "a.pl:visited { color : #505050; text-decoration : none; font-size: 7px;}" );
2412         w.write( SurfacingConstants.NL );
2413         w.write( "a.pl:link { color : #505050; text-decoration : none; font-size: 7px;}" );
2414         w.write( SurfacingConstants.NL );
2415         w.write( "a.pl:active { color : #505050; text-decoration : none; font-size: 7px;}" );
2416         w.write( SurfacingConstants.NL );
2417         w.write( "a.pl:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
2418         w.write( SurfacingConstants.NL );
2419         //
2420         w.write( "a.ps:visited { color : #707070; text-decoration : none; font-size: 7px;}" );
2421         w.write( SurfacingConstants.NL );
2422         w.write( "a.ps:link { color : #707070; text-decoration : none; font-size: 7px;}" );
2423         w.write( SurfacingConstants.NL );
2424         w.write( "a.ps:active { color : #707070; text-decoration : none; font-size: 7px;}" );
2425         w.write( SurfacingConstants.NL );
2426         w.write( "a.ps:hover { color : #FFFFFF; background-color : #000000; text-decoration : none; font-size: 7px;}" );
2427         w.write( SurfacingConstants.NL );
2428         //
2429         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
2430         w.write( SurfacingConstants.NL );
2431         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
2432         w.write( SurfacingConstants.NL );
2433         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
2434         w.write( SurfacingConstants.NL );
2435         w.write( "</style>" );
2436         w.write( SurfacingConstants.NL );
2437         w.write( "</head>" );
2438         w.write( SurfacingConstants.NL );
2439     }
2440
2441     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2442                                           final String filename,
2443                                           final Format format ) {
2444         final File outfile = new File( filename );
2445         checkForOutputFileWriteability( outfile );
2446         try {
2447             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2448             matrix.toWriter( out, format );
2449             out.flush();
2450             out.close();
2451         }
2452         catch ( final IOException e ) {
2453             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2454         }
2455         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2456     }
2457
2458     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2459         checkForOutputFileWriteability( matrix_outfile );
2460         try {
2461             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2462             for( final DistanceMatrix distance_matrix : matrices ) {
2463                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2464                 out.write( ForesterUtil.LINE_SEPARATOR );
2465                 out.flush();
2466             }
2467             out.close();
2468         }
2469         catch ( final IOException e ) {
2470             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2471         }
2472         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2473     }
2474
2475     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2476         final PhylogenyWriter writer = new PhylogenyWriter();
2477         try {
2478             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2479         }
2480         catch ( final IOException e ) {
2481             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
2482                     + e );
2483         }
2484         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2485     }
2486
2487     public static void writePresentToNexus( final File output_file,
2488                                             final File positive_filter_file,
2489                                             final SortedSet<String> filter,
2490                                             final List<GenomeWideCombinableDomains> gwcd_list ) {
2491         try {
2492             writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfDomainPresenceOrAbsence( gwcd_list,
2493                                                                                                 positive_filter_file == null ? null
2494                                                                                                         : filter ),
2495                                output_file + surfacing.DOMAINS_PRESENT_NEXUS,
2496                                Format.NEXUS_BINARY );
2497             writeMatrixToFile( DomainParsimonyCalculator.createMatrixOfBinaryDomainCombinationPresenceOrAbsence( gwcd_list ),
2498                                output_file + surfacing.BDC_PRESENT_NEXUS,
2499                                Format.NEXUS_BINARY );
2500         }
2501         catch ( final Exception e ) {
2502             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2503         }
2504     }
2505
2506     public static void writeProteinListsForAllSpecies( final File output_dir,
2507                                                        final SortedMap<Species, List<Protein>> protein_lists_per_species,
2508                                                        final List<GenomeWideCombinableDomains> gwcd_list,
2509                                                        final double domain_e_cutoff ) {
2510         final SortedSet<String> all_domains = new TreeSet<String>();
2511         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
2512             all_domains.addAll( gwcd.getAllDomainIds() );
2513         }
2514         for( final String domain : all_domains ) {
2515             final File out = new File( output_dir + ForesterUtil.FILE_SEPARATOR + domain + surfacing.SEQ_EXTRACT_SUFFIX );
2516             checkForOutputFileWriteability( out );
2517             try {
2518                 final Writer proteins_file_writer = new BufferedWriter( new FileWriter( out ) );
2519                 extractProteinNames( protein_lists_per_species,
2520                                      domain,
2521                                      proteins_file_writer,
2522                                      "\t",
2523                                      surfacing.LIMIT_SPEC_FOR_PROT_EX,
2524                                      domain_e_cutoff );
2525                 proteins_file_writer.close();
2526             }
2527             catch ( final IOException e ) {
2528                 ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
2529             }
2530             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote proteins list to \"" + out + "\"" );
2531         }
2532     }
2533
2534     public static void writeTaxonomyLinks( final Writer writer,
2535                                            final String species,
2536                                            final Map<String, Integer> tax_code_to_id_map ) throws IOException {
2537         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2538             writer.write( " [" );
2539             if ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( species ) ) {
2540                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
2541                         + tax_code_to_id_map.get( species ) + "\" target=\"taxonomy_window\">uniprot</a>" );
2542             }
2543             else {
2544                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2545                         + "\" target=\"taxonomy_window\">eol</a>" );
2546                 writer.write( "|" );
2547                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + species
2548                         + "\" target=\"taxonomy_window\">scholar</a>" );
2549                 writer.write( "|" );
2550                 writer.write( "<a href=\"" + SurfacingConstants.GOOGLE_WEB_SEARCH_LINK + species
2551                         + "\" target=\"taxonomy_window\">google</a>" );
2552             }
2553             writer.write( "]" );
2554         }
2555     }
2556
2557     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
2558         if ( map.containsKey( s ) ) {
2559             map.put( s, map.get( s ) + 1 );
2560         }
2561         else {
2562             map.put( s, 1 );
2563         }
2564     }
2565
2566     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
2567                                                                     final String outfilename_for_counts,
2568                                                                     final String outfilename_for_dc,
2569                                                                     final String outfilename_for_dc_for_go_mapping,
2570                                                                     final String outfilename_for_dc_for_go_mapping_unique,
2571                                                                     final String outfilename_for_rank_counts,
2572                                                                     final String outfilename_for_ancestor_species_counts,
2573                                                                     final String outfilename_for_protein_stats,
2574                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
2575                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
2576                                                                     final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
2577         try {
2578             //
2579             //            if ( protein_length_stats_by_dc != null ) {
2580             //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
2581             //                    System.out.print( entry.getKey().toString() );
2582             //                    System.out.print( ": " );
2583             //                    double[] a = entry.getValue().getDataAsDoubleArray();
2584             //                    for( int i = 0; i < a.length; i++ ) {
2585             //                        System.out.print( a[ i ] + " " );
2586             //                    }
2587             //                    System.out.println();
2588             //                }
2589             //            }
2590             //            if ( domain_number_stats_by_dc != null ) {
2591             //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
2592             //                    System.out.print( entry.getKey().toString() );
2593             //                    System.out.print( ": " );
2594             //                    double[] a = entry.getValue().getDataAsDoubleArray();
2595             //                    for( int i = 0; i < a.length; i++ ) {
2596             //                        System.out.print( a[ i ] + " " );
2597             //                    }
2598             //                    System.out.println();
2599             //                }
2600             //            }
2601             //
2602             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
2603             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
2604             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
2605             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
2606             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
2607             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
2608                 final PhylogenyNode n = it.next();
2609                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
2610                 for( final String dc : gained_dc ) {
2611                     if ( dc_gain_counts.containsKey( dc ) ) {
2612                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
2613                     }
2614                     else {
2615                         dc_gain_counts.put( dc, 1 );
2616                     }
2617                 }
2618             }
2619             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
2620             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
2621             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
2622             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
2623             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
2624             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
2625             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
2626             final Set<String> dcs = dc_gain_counts.keySet();
2627             final SortedSet<String> more_than_once = new TreeSet<String>();
2628             DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
2629             DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
2630             DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
2631             final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
2632             long gained_multiple_times_domain_length_sum = 0;
2633             long gained_once_domain_length_sum = 0;
2634             long gained_multiple_times_domain_length_count = 0;
2635             long gained_once_domain_length_count = 0;
2636             for( final String dc : dcs ) {
2637                 final int count = dc_gain_counts.get( dc );
2638                 if ( histogram.containsKey( count ) ) {
2639                     histogram.put( count, histogram.get( count ) + 1 );
2640                     domain_lists.get( count ).append( ", " + dc );
2641                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
2642                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
2643                 }
2644                 else {
2645                     histogram.put( count, 1 );
2646                     domain_lists.put( count, new StringBuilder( dc ) );
2647                     final PriorityQueue<String> q = new PriorityQueue<String>();
2648                     q.addAll( splitDomainCombination( dc ) );
2649                     domain_lists_go.put( count, q );
2650                     final SortedSet<String> set = new TreeSet<String>();
2651                     set.addAll( splitDomainCombination( dc ) );
2652                     domain_lists_go_unique.put( count, set );
2653                 }
2654                 if ( protein_length_stats_by_dc != null ) {
2655                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
2656                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
2657                     }
2658                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
2659                             .arithmeticMean() );
2660                 }
2661                 if ( domain_number_stats_by_dc != null ) {
2662                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
2663                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
2664                     }
2665                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
2666                             .arithmeticMean() );
2667                 }
2668                 if ( domain_length_stats_by_domain != null ) {
2669                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
2670                         dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
2671                     }
2672                     final String[] ds = dc.split( "=" );
2673                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2674                             .get( ds[ 0 ] ).arithmeticMean() );
2675                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
2676                             .get( ds[ 1 ] ).arithmeticMean() );
2677                 }
2678                 if ( count > 1 ) {
2679                     more_than_once.add( dc );
2680                     if ( protein_length_stats_by_dc != null ) {
2681                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2682                         for( final double element : s.getData() ) {
2683                             gained_multiple_times_lengths_stats.addValue( element );
2684                         }
2685                     }
2686                     if ( domain_number_stats_by_dc != null ) {
2687                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2688                         for( final double element : s.getData() ) {
2689                             gained_multiple_times_domain_count_stats.addValue( element );
2690                         }
2691                     }
2692                     if ( domain_length_stats_by_domain != null ) {
2693                         final String[] ds = dc.split( "=" );
2694                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2695                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2696                         for( final double element : s0.getData() ) {
2697                             gained_multiple_times_domain_length_sum += element;
2698                             ++gained_multiple_times_domain_length_count;
2699                         }
2700                         for( final double element : s1.getData() ) {
2701                             gained_multiple_times_domain_length_sum += element;
2702                             ++gained_multiple_times_domain_length_count;
2703                         }
2704                     }
2705                 }
2706                 else {
2707                     if ( protein_length_stats_by_dc != null ) {
2708                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
2709                         for( final double element : s.getData() ) {
2710                             gained_once_lengths_stats.addValue( element );
2711                         }
2712                     }
2713                     if ( domain_number_stats_by_dc != null ) {
2714                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
2715                         for( final double element : s.getData() ) {
2716                             gained_once_domain_count_stats.addValue( element );
2717                         }
2718                     }
2719                     if ( domain_length_stats_by_domain != null ) {
2720                         final String[] ds = dc.split( "=" );
2721                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
2722                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
2723                         for( final double element : s0.getData() ) {
2724                             gained_once_domain_length_sum += element;
2725                             ++gained_once_domain_length_count;
2726                         }
2727                         for( final double element : s1.getData() ) {
2728                             gained_once_domain_length_sum += element;
2729                             ++gained_once_domain_length_count;
2730                         }
2731                     }
2732                 }
2733             }
2734             final Set<Integer> histogram_keys = histogram.keySet();
2735             for( final Integer histogram_key : histogram_keys ) {
2736                 final int count = histogram.get( histogram_key );
2737                 final StringBuilder dc = domain_lists.get( histogram_key );
2738                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
2739                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
2740                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2741                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
2742                 Arrays.sort( sorted );
2743                 for( final Object domain : sorted ) {
2744                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
2745                 }
2746                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
2747                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
2748                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
2749                 }
2750             }
2751             out_counts.close();
2752             out_dc.close();
2753             out_dc_for_go_mapping.close();
2754             out_dc_for_go_mapping_unique.close();
2755             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
2756             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
2757             for( final String dc : more_than_once ) {
2758                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
2759                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
2760                     final PhylogenyNode n = it.next();
2761                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
2762                         nodes.add( n );
2763                     }
2764                 }
2765                 for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
2766                     for( int j = i + 1; j < nodes.size(); ++j ) {
2767                         final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
2768                         String rank = "unknown";
2769                         if ( lca.getNodeData().isHasTaxonomy()
2770                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
2771                             rank = lca.getNodeData().getTaxonomy().getRank();
2772                         }
2773                         addToCountMap( lca_rank_counts, rank );
2774                         String lca_species;
2775                         if ( lca.getNodeData().isHasTaxonomy()
2776                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
2777                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
2778                         }
2779                         else if ( lca.getNodeData().isHasTaxonomy()
2780                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
2781                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
2782                         }
2783                         else {
2784                             lca_species = lca.getName();
2785                         }
2786                         addToCountMap( lca_ancestor_species_counts, lca_species );
2787                     }
2788                 }
2789             }
2790             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
2791             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
2792             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
2793             ForesterUtil.map2writer( out_for_ancestor_species_counts,
2794                                      lca_ancestor_species_counts,
2795                                      "\t",
2796                                      ForesterUtil.LINE_SEPARATOR );
2797             out_for_rank_counts.close();
2798             out_for_ancestor_species_counts.close();
2799             if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
2800                     && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
2801                 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
2802                 w.write( "Domain Lengths: " );
2803                 w.write( "\n" );
2804                 if ( domain_length_stats_by_domain != null ) {
2805                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
2806                             .entrySet() ) {
2807                         w.write( entry.getKey().toString() );
2808                         w.write( "\t" + entry.getValue().arithmeticMean() );
2809                         w.write( "\t" + entry.getValue().median() );
2810                         w.write( "\n" );
2811                     }
2812                 }
2813                 w.flush();
2814                 w.write( "\n" );
2815                 w.write( "\n" );
2816                 w.write( "Protein Lengths: " );
2817                 w.write( "\n" );
2818                 if ( protein_length_stats_by_dc != null ) {
2819                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
2820                             .entrySet() ) {
2821                         w.write( entry.getKey().toString() );
2822                         w.write( "\t" + entry.getValue().arithmeticMean() );
2823                         w.write( "\t" + entry.getValue().median() );
2824                         w.write( "\n" );
2825                     }
2826                 }
2827                 w.flush();
2828                 w.write( "\n" );
2829                 w.write( "\n" );
2830                 w.write( "Number of domains: " );
2831                 w.write( "\n" );
2832                 if ( domain_number_stats_by_dc != null ) {
2833                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
2834                             .entrySet() ) {
2835                         w.write( entry.getKey().toString() );
2836                         w.write( "\t" + entry.getValue().arithmeticMean() );
2837                         w.write( "\t" + entry.getValue().median() );
2838                         w.write( "\n" );
2839                     }
2840                 }
2841                 w.flush();
2842                 w.write( "\n" );
2843                 w.write( "\n" );
2844                 w.write( "Gained once, domain lengths:" );
2845                 w.write( "\n" );
2846                 w.write( "N: " + gained_once_domain_length_count );
2847                 w.write( "\n" );
2848                 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
2849                 w.write( "\n" );
2850                 w.write( "\n" );
2851                 w.write( "Gained multiple times, domain lengths:" );
2852                 w.write( "\n" );
2853                 w.write( "N: " + gained_multiple_times_domain_length_count );
2854                 w.write( "\n" );
2855                 w.write( "Avg: "
2856                         + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
2857                 w.write( "\n" );
2858                 w.write( "\n" );
2859                 w.write( "\n" );
2860                 w.write( "\n" );
2861                 w.write( "Gained once, protein lengths:" );
2862                 w.write( "\n" );
2863                 w.write( gained_once_lengths_stats.toString() );
2864                 gained_once_lengths_stats = null;
2865                 w.write( "\n" );
2866                 w.write( "\n" );
2867                 w.write( "Gained once, domain counts:" );
2868                 w.write( "\n" );
2869                 w.write( gained_once_domain_count_stats.toString() );
2870                 gained_once_domain_count_stats = null;
2871                 w.write( "\n" );
2872                 w.write( "\n" );
2873                 w.write( "Gained multiple times, protein lengths:" );
2874                 w.write( "\n" );
2875                 w.write( gained_multiple_times_lengths_stats.toString() );
2876                 gained_multiple_times_lengths_stats = null;
2877                 w.write( "\n" );
2878                 w.write( "\n" );
2879                 w.write( "Gained multiple times, domain counts:" );
2880                 w.write( "\n" );
2881                 w.write( gained_multiple_times_domain_count_stats.toString() );
2882                 w.flush();
2883                 w.close();
2884             }
2885         }
2886         catch ( final IOException e ) {
2887             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2888         }
2889         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
2890                 + outfilename_for_counts + "]" );
2891         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
2892                 + outfilename_for_dc + "]" );
2893         ForesterUtil.programMessage( surfacing.PRG_NAME,
2894                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
2895                                              + outfilename_for_dc_for_go_mapping + "]" );
2896         ForesterUtil.programMessage( surfacing.PRG_NAME,
2897                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
2898                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
2899     }
2900
2901     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
2902                                                                         final boolean get_gains ) {
2903         final SortedSet<String> domains = new TreeSet<String>();
2904         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
2905             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
2906             if ( get_gains ) {
2907                 domains.addAll( chars.getGainedCharacters() );
2908             }
2909             else {
2910                 domains.addAll( chars.getLostCharacters() );
2911             }
2912         }
2913         return domains;
2914     }
2915
2916     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
2917                                                             final boolean domain_combinations,
2918                                                             final CharacterStateMatrix.GainLossStates state,
2919                                                             final String outfile ) {
2920         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
2921                 + ForesterUtil.FILE_SEPARATOR + base_dir );
2922         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2923             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2924         }
2925         if ( domain_combinations ) {
2926             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2927                     + ForesterUtil.FILE_SEPARATOR + "DC" );
2928         }
2929         else {
2930             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2931                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
2932         }
2933         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2934             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2935         }
2936         if ( state == GainLossStates.GAIN ) {
2937             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2938                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
2939         }
2940         else if ( state == GainLossStates.LOSS ) {
2941             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2942                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
2943         }
2944         else {
2945             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
2946                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
2947         }
2948         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
2949             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
2950         }
2951         return per_node_go_mapped_domain_gain_loss_files_base_dir;
2952     }
2953
2954     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
2955         final SortedMap<String, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
2956         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
2957         for( final String domain_id : cds.keySet() ) {
2958             final CombinableDomains cd = cds.get( domain_id );
2959             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
2960         }
2961         return binary_combinations;
2962     }
2963
2964     private static void printSomeStats( final DescriptiveStatistics stats, final AsciiHistogram histo, final Writer w )
2965             throws IOException {
2966         w.write( "<hr>" );
2967         w.write( "<br>" );
2968         w.write( SurfacingConstants.NL );
2969         w.write( "<tt><pre>" );
2970         w.write( SurfacingConstants.NL );
2971         if ( histo != null ) {
2972             w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2973             w.write( SurfacingConstants.NL );
2974         }
2975         w.write( "</pre></tt>" );
2976         w.write( SurfacingConstants.NL );
2977         w.write( "<table>" );
2978         w.write( SurfacingConstants.NL );
2979         w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2980         w.write( SurfacingConstants.NL );
2981         w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2982         w.write( SurfacingConstants.NL );
2983         w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2984         w.write( SurfacingConstants.NL );
2985         w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2986         w.write( SurfacingConstants.NL );
2987         if ( stats.getN() > 1 ) {
2988             w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2989         }
2990         else {
2991             w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2992         }
2993         w.write( SurfacingConstants.NL );
2994         w.write( "</table>" );
2995         w.write( SurfacingConstants.NL );
2996         w.write( "<br>" );
2997         w.write( SurfacingConstants.NL );
2998     }
2999
3000     private static List<String> splitDomainCombination( final String dc ) {
3001         final String[] s = dc.split( "=" );
3002         if ( s.length != 2 ) {
3003             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
3004                     + dc );
3005             System.exit( -1 );
3006         }
3007         final List<String> l = new ArrayList<String>( 2 );
3008         l.add( s[ 0 ] );
3009         l.add( s[ 1 ] );
3010         return l;
3011     }
3012
3013     private static void writeAllEncounteredPfamsToFile( final Map<String, List<GoId>> domain_id_to_go_ids_map,
3014                                                         final Map<GoId, GoTerm> go_id_to_term_map,
3015                                                         final String outfile_name,
3016                                                         final SortedSet<String> all_pfams_encountered ) {
3017         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
3018         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
3019                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
3020         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
3021         int biological_process_counter = 0;
3022         int cellular_component_counter = 0;
3023         int molecular_function_counter = 0;
3024         int pfams_with_mappings_counter = 0;
3025         int pfams_without_mappings_counter = 0;
3026         int pfams_without_mappings_to_bp_or_mf_counter = 0;
3027         int pfams_with_mappings_to_bp_or_mf_counter = 0;
3028         try {
3029             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
3030             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
3031             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
3032             summary_writer.write( "# Pfam to GO mapping summary" );
3033             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3034             summary_writer.write( "# Actual summary is at the end of this file." );
3035             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3036             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
3037             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3038             for( final String pfam : all_pfams_encountered ) {
3039                 all_pfams_encountered_writer.write( pfam );
3040                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
3041                 final String domain_id = new String( pfam );
3042                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
3043                     ++pfams_with_mappings_counter;
3044                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
3045                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
3046                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
3047                     boolean maps_to_bp = false;
3048                     boolean maps_to_cc = false;
3049                     boolean maps_to_mf = false;
3050                     for( final GoId go_id : go_ids ) {
3051                         final GoTerm go_term = go_id_to_term_map.get( go_id );
3052                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
3053                             maps_to_bp = true;
3054                         }
3055                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
3056                             maps_to_cc = true;
3057                         }
3058                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
3059                             maps_to_mf = true;
3060                         }
3061                     }
3062                     if ( maps_to_bp ) {
3063                         ++biological_process_counter;
3064                     }
3065                     if ( maps_to_cc ) {
3066                         ++cellular_component_counter;
3067                     }
3068                     if ( maps_to_mf ) {
3069                         ++molecular_function_counter;
3070                     }
3071                     if ( maps_to_bp || maps_to_mf ) {
3072                         ++pfams_with_mappings_to_bp_or_mf_counter;
3073                     }
3074                     else {
3075                         ++pfams_without_mappings_to_bp_or_mf_counter;
3076                     }
3077                 }
3078                 else {
3079                     ++pfams_without_mappings_to_bp_or_mf_counter;
3080                     ++pfams_without_mappings_counter;
3081                     summary_writer.write( pfam );
3082                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3083                 }
3084             }
3085             all_pfams_encountered_writer.close();
3086             all_pfams_encountered_with_go_annotation_writer.close();
3087             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
3088                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
3089             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
3090                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
3091                     + "\"" );
3092             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
3093                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
3094                     + encountered_pfams_summary_file + "\"" );
3095             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
3096                     + all_pfams_encountered.size() );
3097             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
3098                     + pfams_without_mappings_counter + " ["
3099                     + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3100             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
3101                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
3102                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3103             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
3104                     + pfams_with_mappings_counter + " ["
3105                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3106             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
3107                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
3108                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3109             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
3110                     + biological_process_counter + " ["
3111                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
3112             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
3113                     + molecular_function_counter + " ["
3114                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
3115             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
3116                     + cellular_component_counter + " ["
3117                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
3118             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3119             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
3120             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3121             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
3122                     + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3123             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3124             summary_writer.write( "# Pfams without mapping to proc. or func. : "
3125                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
3126                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3127             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3128             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
3129                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
3130             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3131             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
3132                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
3133                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
3134             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3135             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
3136                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
3137             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3138             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
3139                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
3140             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3141             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
3142                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
3143             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
3144             summary_writer.close();
3145         }
3146         catch ( final IOException e ) {
3147             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
3148         }
3149     }
3150
3151     private final static void writeColorLabels( final String l, final Color c, final Writer w ) throws IOException {
3152         w.write( "<tr><td><b><span style=\"color:" );
3153         w.write( String.format( "#%02x%02x%02x", c.getRed(), c.getGreen(), c.getBlue() ) );
3154         w.write( "\">" );
3155         w.write( l );
3156         w.write( "</span></b></td></tr>" );
3157         w.write( SurfacingConstants.NL );
3158     }
3159
3160     private static void writeDomainData( final Map<String, List<GoId>> domain_id_to_go_ids_map,
3161                                          final Map<GoId, GoTerm> go_id_to_term_map,
3162                                          final GoNameSpace go_namespace_limit,
3163                                          final Writer out,
3164                                          final String domain_0,
3165                                          final String domain_1,
3166                                          final String prefix_for_html,
3167                                          final String character_separator_for_non_html_output,
3168                                          final Map<String, Set<String>>[] domain_id_to_secondary_features_maps,
3169                                          final Set<GoId> all_go_ids ) throws IOException {
3170         boolean any_go_annotation_present = false;
3171         boolean first_has_no_go = false;
3172         int domain_count = 2; // To distinguish between domains and binary domain combinations.
3173         if ( ForesterUtil.isEmpty( domain_1 ) ) {
3174             domain_count = 1;
3175         }
3176         // The following has a difficult to understand logic.
3177         for( int d = 0; d < domain_count; ++d ) {
3178             List<GoId> go_ids = null;
3179             boolean go_annotation_present = false;
3180             if ( d == 0 ) {
3181                 if ( domain_id_to_go_ids_map.containsKey( domain_0 ) ) {
3182                     go_annotation_present = true;
3183                     any_go_annotation_present = true;
3184                     go_ids = domain_id_to_go_ids_map.get( domain_0 );
3185                 }
3186                 else {
3187                     first_has_no_go = true;
3188                 }
3189             }
3190             else {
3191                 if ( domain_id_to_go_ids_map.containsKey( domain_1 ) ) {
3192                     go_annotation_present = true;
3193                     any_go_annotation_present = true;
3194                     go_ids = domain_id_to_go_ids_map.get( domain_1 );
3195                 }
3196             }
3197             if ( go_annotation_present ) {
3198                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
3199                 for( final GoId go_id : go_ids ) {
3200                     out.write( "<tr>" );
3201                     if ( first ) {
3202                         first = false;
3203                         writeDomainIdsToHtml( out,
3204                                               domain_0,
3205                                               domain_1,
3206                                               prefix_for_html,
3207                                               domain_id_to_secondary_features_maps );
3208                     }
3209                     else {
3210                         out.write( "<td></td>" );
3211                     }
3212                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
3213                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
3214                     }
3215                     final GoTerm go_term = go_id_to_term_map.get( go_id );
3216                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
3217                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
3218                         final String go_id_str = go_id.getId();
3219                         out.write( "<td>" );
3220                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
3221                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
3222                         out.write( "</td><td>" );
3223                         out.write( go_term.getName() );
3224                         if ( domain_count == 2 ) {
3225                             out.write( " (" + d + ")" );
3226                         }
3227                         out.write( "</td><td>" );
3228                         // out.write( top );
3229                         // out.write( "</td><td>" );
3230                         out.write( "[" );
3231                         out.write( go_term.getGoNameSpace().toShortString() );
3232                         out.write( "]" );
3233                         out.write( "</td>" );
3234                         if ( all_go_ids != null ) {
3235                             all_go_ids.add( go_id );
3236                         }
3237                     }
3238                     else {
3239                         out.write( "<td>" );
3240                         out.write( "</td><td>" );
3241                         out.write( "</td><td>" );
3242                         out.write( "</td><td>" );
3243                         out.write( "</td>" );
3244                     }
3245                     out.write( "</tr>" );
3246                     out.write( SurfacingConstants.NL );
3247                 }
3248             }
3249         } //  for( int d = 0; d < domain_count; ++d )
3250         if ( !any_go_annotation_present ) {
3251             out.write( "<tr>" );
3252             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
3253             out.write( "<td>" );
3254             out.write( "</td><td>" );
3255             out.write( "</td><td>" );
3256             out.write( "</td><td>" );
3257             out.write( "</td>" );
3258             out.write( "</tr>" );
3259             out.write( SurfacingConstants.NL );
3260         }
3261     }
3262
3263     private static void writeDomainIdsToHtml( final Writer out,
3264                                               final String domain_0,
3265                                               final String domain_1,
3266                                               final String prefix_for_detailed_html,
3267                                               final Map<String, Set<String>>[] domain_id_to_secondary_features_maps )
3268             throws IOException {
3269         out.write( "<td>" );
3270         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
3271             out.write( prefix_for_detailed_html );
3272             out.write( " " );
3273         }
3274         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
3275         out.write( "</td>" );
3276     }
3277
3278     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
3279                                                                  final String domain_0,
3280                                                                  final String domain_1 ) throws IOException {
3281         individual_files_writer.write( domain_0 );
3282         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
3283         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
3284             individual_files_writer.write( domain_1 );
3285             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
3286         }
3287     }
3288
3289     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
3290         try {
3291             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
3292             for( final String pfam : pfams ) {
3293                 writer.write( pfam );
3294                 writer.write( ForesterUtil.LINE_SEPARATOR );
3295             }
3296             writer.close();
3297             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
3298                     + "]" );
3299         }
3300         catch ( final IOException e ) {
3301             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
3302         }
3303     }
3304
3305     private static void writeToNexus( final String outfile_name,
3306                                       final CharacterStateMatrix<BinaryStates> matrix,
3307                                       final Phylogeny phylogeny ) {
3308         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
3309             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
3310                     + "] to nexus" );
3311         }
3312         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
3313         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
3314         phylogenies.add( phylogeny );
3315         try {
3316             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
3317             w.write( NexusConstants.NEXUS );
3318             w.write( ForesterUtil.LINE_SEPARATOR );
3319             my_matrix.writeNexusTaxaBlock( w );
3320             my_matrix.writeNexusBinaryChractersBlock( w );
3321             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
3322             w.flush();
3323             w.close();
3324             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
3325         }
3326         catch ( final IOException e ) {
3327             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
3328         }
3329     }
3330
3331     private static void writeToNexus( final String outfile_name,
3332                                       final DomainParsimonyCalculator domain_parsimony,
3333                                       final Phylogeny phylogeny ) {
3334         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
3335                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
3336                       phylogeny );
3337         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
3338                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
3339                       phylogeny );
3340     }
3341
3342     final static class DomainComparator implements Comparator<Domain> {
3343
3344         final private boolean _ascending;
3345
3346         public DomainComparator( final boolean ascending ) {
3347             _ascending = ascending;
3348         }
3349
3350         @Override
3351         public final int compare( final Domain d0, final Domain d1 ) {
3352             if ( d0.getFrom() < d1.getFrom() ) {
3353                 return _ascending ? -1 : 1;
3354             }
3355             else if ( d0.getFrom() > d1.getFrom() ) {
3356                 return _ascending ? 1 : -1;
3357             }
3358             return 0;
3359         }
3360     }
3361 }