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.io.BufferedWriter;
  30 import java.io.File;
  31 import java.io.FileWriter;
  32 import java.io.IOException;
  33 import java.io.Writer;
  34 import java.text.DecimalFormat;
  35 import java.text.NumberFormat;
  36 import java.util.ArrayList;
  37 import java.util.Arrays;
  38 import java.util.Collections;
  39 import java.util.Comparator;
  40 import java.util.HashMap;
  41 import java.util.HashSet;
  42 import java.util.Iterator;
  43 import java.util.List;
  44 import java.util.Map;
  45 import java.util.Map.Entry;
  46 import java.util.PriorityQueue;
  47 import java.util.Set;
  48 import java.util.SortedMap;
  49 import java.util.SortedSet;
  50 import java.util.TreeMap;
  51 import java.util.TreeSet;
  52 import java.util.regex.Matcher;
  53 import java.util.regex.Pattern;
  54
  55 import org.forester.application.surfacing;
  56 import org.forester.evoinference.distance.NeighborJoining;
  57 import org.forester.evoinference.matrix.character.BasicCharacterStateMatrix;
  58 import org.forester.evoinference.matrix.character.CharacterStateMatrix;
  59 import org.forester.evoinference.matrix.character.CharacterStateMatrix.BinaryStates;
  60 import org.forester.evoinference.matrix.character.CharacterStateMatrix.Format;
  61 import org.forester.evoinference.matrix.character.CharacterStateMatrix.GainLossStates;
  62 import org.forester.evoinference.matrix.distance.BasicSymmetricalDistanceMatrix;
  63 import org.forester.evoinference.matrix.distance.DistanceMatrix;
  64 import org.forester.go.GoId;
  65 import org.forester.go.GoNameSpace;
  66 import org.forester.go.GoTerm;
  67 import org.forester.go.PfamToGoMapping;
  68 import org.forester.io.parsers.nexus.NexusConstants;
  69 import org.forester.io.writers.PhylogenyWriter;
  70 import org.forester.phylogeny.Phylogeny;
  71 import org.forester.phylogeny.PhylogenyMethods;
  72 import org.forester.phylogeny.PhylogenyNode;
  73 import org.forester.phylogeny.PhylogenyNode.NH_CONVERSION_SUPPORT_VALUE_STYLE;
  74 import org.forester.phylogeny.data.BinaryCharacters;
  75 import org.forester.phylogeny.data.Confidence;
  76 import org.forester.phylogeny.iterators.PhylogenyNodeIterator;
  77 import org.forester.protein.BasicDomain;
  78 import org.forester.protein.BasicProtein;
  79 import org.forester.protein.BinaryDomainCombination;
  80 import org.forester.protein.Domain;
  81 import org.forester.protein.DomainId;
  82 import org.forester.protein.Protein;
  83 import org.forester.species.Species;
  84 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  85 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  86 import org.forester.surfacing.GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder;
  87 import org.forester.util.AsciiHistogram;
  88 import org.forester.util.BasicDescriptiveStatistics;
  89 import org.forester.util.BasicTable;
  90 import org.forester.util.BasicTableParser;
  91 import org.forester.util.DescriptiveStatistics;
  92 import org.forester.util.ForesterUtil;
  93
  94 public final class SurfacingUtil {
  95
  96     private final static NumberFormat       FORMATTER                        = new DecimalFormat( "0.0E0" );
  97     private final static NumberFormat       FORMATTER_3                      = new DecimalFormat( "0.000" );
  98     private static final Comparator<Domain> ASCENDING_CONFIDENCE_VALUE_ORDER = new Comparator<Domain>() {
  99
 100                                                                                  @Override
 101                                                                                  public int compare( final Domain d1,
 102                                                                                                      final Domain d2 ) {
 103                                                                                      if ( d1.getPerSequenceEvalue() < d2
 104                                                                                              .getPerSequenceEvalue() ) {
 105                                                                                          return -1;
 106                                                                                      }
 107                                                                                      else if ( d1
 108                                                                                              .getPerSequenceEvalue() > d2
 109                                                                                              .getPerSequenceEvalue() ) {
 110                                                                                          return 1;
 111                                                                                      }
 112                                                                                      else {
 113                                                                                          return d1.compareTo( d2 );
 114                                                                                      }
 115                                                                                  }
 116                                                                              };
 117     public final static Pattern             PATTERN_SP_STYLE_TAXONOMY        = Pattern.compile( "^[A-Z0-9]{3,5}$" );
 118     private static final boolean            USE_LAST                         = true;
 119
 120     private SurfacingUtil() {
 121         // Hidden constructor.
 122     }
 123
 124     public static void performDomainArchitectureAnalysis( final SortedMap<String, Set<String>> domain_architecutures,
 125                                                           final SortedMap<String, Integer> domain_architecuture_counts,
 126                                                           final int min_count,
 127                                                           final File da_counts_outfile,
 128                                                           final File unique_da_outfile ) {
 129         checkForOutputFileWriteability( da_counts_outfile );
 130         checkForOutputFileWriteability( unique_da_outfile );
 131         try {
 132             final BufferedWriter da_counts_out = new BufferedWriter( new FileWriter( da_counts_outfile ) );
 133             final BufferedWriter unique_da_out = new BufferedWriter( new FileWriter( unique_da_outfile ) );
 134             final Iterator<Entry<String, Integer>> it = domain_architecuture_counts.entrySet().iterator();
 135             while ( it.hasNext() ) {
 136                 final Map.Entry<String, Integer> e = it.next();
 137                 final String da = e.getKey();
 138                 final int count = e.getValue();
 139                 if ( count >= min_count ) {
 140                     da_counts_out.write( da );
 141                     da_counts_out.write( "\t" );
 142                     da_counts_out.write( String.valueOf( count ) );
 143                     da_counts_out.write( ForesterUtil.LINE_SEPARATOR );
 144                 }
 145                 if ( count == 1 ) {
 146                     final Iterator<Entry<String, Set<String>>> it2 = domain_architecutures.entrySet().iterator();
 147                     while ( it2.hasNext() ) {
 148                         final Map.Entry<String, Set<String>> e2 = it2.next();
 149                         final String genome = e2.getKey();
 150                         final Set<String> das = e2.getValue();
 151                         if ( das.contains( da ) ) {
 152                             unique_da_out.write( genome );
 153                             unique_da_out.write( "\t" );
 154                             unique_da_out.write( da );
 155                             unique_da_out.write( ForesterUtil.LINE_SEPARATOR );
 156                         }
 157                     }
 158                 }
 159             }
 160             unique_da_out.close();
 161             da_counts_out.close();
 162         }
 163         catch ( final IOException e ) {
 164             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
 165         }
 166         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + da_counts_outfile + "\"" );
 167         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + unique_da_outfile + "\"" );
 168         //
 169     }
 170
 171     public static int storeDomainArchitectures( final String genome,
 172                                                 final SortedMap<String, Set<String>> domain_architecutures,
 173                                                 final List<Protein> protein_list,
 174                                                 final Map<String, Integer> distinct_domain_architecuture_counts ) {
 175         final Set<String> da = new HashSet<String>();
 176         domain_architecutures.put( genome, da );
 177         for( final Protein protein : protein_list ) {
 178             final String da_str = ( ( BasicProtein ) protein ).toDomainArchitectureString( "~", 3, "=" );
 179             if ( !da.contains( da_str ) ) {
 180                 if ( !distinct_domain_architecuture_counts.containsKey( da_str ) ) {
 181                     distinct_domain_architecuture_counts.put( da_str, 1 );
 182                 }
 183                 else {
 184                     distinct_domain_architecuture_counts.put( da_str,
 185                                                               distinct_domain_architecuture_counts.get( da_str ) + 1 );
 186                 }
 187                 da.add( da_str );
 188             }
 189         }
 190         return da.size();
 191     }
 192
 193     public static void addAllBinaryDomainCombinationToSet( final GenomeWideCombinableDomains genome,
 194                                                            final SortedSet<BinaryDomainCombination> binary_domain_combinations ) {
 195         final SortedMap<DomainId, CombinableDomains> all_cd = genome.getAllCombinableDomainsIds();
 196         for( final DomainId domain_id : all_cd.keySet() ) {
 197             binary_domain_combinations.addAll( all_cd.get( domain_id ).toBinaryDomainCombinations() );
 198         }
 199     }
 200
 201     public static void addAllDomainIdsToSet( final GenomeWideCombinableDomains genome,
 202                                              final SortedSet<DomainId> domain_ids ) {
 203         final SortedSet<DomainId> domains = genome.getAllDomainIds();
 204         for( final DomainId domain : domains ) {
 205             domain_ids.add( domain );
 206         }
 207     }
 208
 209     public static void addHtmlHead( final Writer w, final String title ) throws IOException {
 210         w.write( SurfacingConstants.NL );
 211         w.write( "<head>" );
 212         w.write( "<title>" );
 213         w.write( title );
 214         w.write( "</title>" );
 215         w.write( SurfacingConstants.NL );
 216         w.write( "<style>" );
 217         w.write( SurfacingConstants.NL );
 218         w.write( "a:visited { color : #6633FF; text-decoration : none; }" );
 219         w.write( SurfacingConstants.NL );
 220         w.write( "a:link { color : #6633FF; text-decoration : none; }" );
 221         w.write( SurfacingConstants.NL );
 222         w.write( "a:active { color : #99FF00; text-decoration : none; }" );
 223         w.write( SurfacingConstants.NL );
 224         w.write( "a:hover { color : #FFFFFF; background-color : #99FF00; text-decoration : none; }" );
 225         w.write( SurfacingConstants.NL );
 226         w.write( "td { text-align: left; vertical-align: top; font-family: Verdana, Arial, Helvetica; font-size: 8pt}" );
 227         w.write( SurfacingConstants.NL );
 228         w.write( "h1 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 18pt; font-weight: bold }" );
 229         w.write( SurfacingConstants.NL );
 230         w.write( "h2 { color : #0000FF; font-family: Verdana, Arial, Helvetica; font-size: 16pt; font-weight: bold }" );
 231         w.write( SurfacingConstants.NL );
 232         w.write( "</style>" );
 233         w.write( SurfacingConstants.NL );
 234         w.write( "</head>" );
 235         w.write( SurfacingConstants.NL );
 236     }
 237
 238     public static DescriptiveStatistics calculateDescriptiveStatisticsForMeanValues( final Set<DomainSimilarity> similarities ) {
 239         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
 240         for( final DomainSimilarity similarity : similarities ) {
 241             stats.addValue( similarity.getMeanSimilarityScore() );
 242         }
 243         return stats;
 244     }
 245
 246     private static void calculateIndependentDomainCombinationGains( final Phylogeny local_phylogeny_l,
 247                                                                     final String outfilename_for_counts,
 248                                                                     final String outfilename_for_dc,
 249                                                                     final String outfilename_for_dc_for_go_mapping,
 250                                                                     final String outfilename_for_dc_for_go_mapping_unique,
 251                                                                     final String outfilename_for_rank_counts,
 252                                                                     final String outfilename_for_ancestor_species_counts,
 253                                                                     final String outfilename_for_protein_stats,
 254                                                                     final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 255                                                                     final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 256                                                                     final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
 257         try {
 258             //
 259             //            if ( protein_length_stats_by_dc != null ) {
 260             //                for( final Entry<?, DescriptiveStatistics> entry : protein_length_stats_by_dc.entrySet() ) {
 261             //                    System.out.print( entry.getKey().toString() );
 262             //                    System.out.print( ": " );
 263             //                    double[] a = entry.getValue().getDataAsDoubleArray();
 264             //                    for( int i = 0; i < a.length; i++ ) {
 265             //                        System.out.print( a[ i ] + " " );
 266             //                    }
 267             //                    System.out.println();
 268             //                }
 269             //            }
 270             //            if ( domain_number_stats_by_dc != null ) {
 271             //                for( final Entry<?, DescriptiveStatistics> entry : domain_number_stats_by_dc.entrySet() ) {
 272             //                    System.out.print( entry.getKey().toString() );
 273             //                    System.out.print( ": " );
 274             //                    double[] a = entry.getValue().getDataAsDoubleArray();
 275             //                    for( int i = 0; i < a.length; i++ ) {
 276             //                        System.out.print( a[ i ] + " " );
 277             //                    }
 278             //                    System.out.println();
 279             //                }
 280             //            }
 281             //
 282             final BufferedWriter out_counts = new BufferedWriter( new FileWriter( outfilename_for_counts ) );
 283             final BufferedWriter out_dc = new BufferedWriter( new FileWriter( outfilename_for_dc ) );
 284             final BufferedWriter out_dc_for_go_mapping = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping ) );
 285             final BufferedWriter out_dc_for_go_mapping_unique = new BufferedWriter( new FileWriter( outfilename_for_dc_for_go_mapping_unique ) );
 286             final SortedMap<String, Integer> dc_gain_counts = new TreeMap<String, Integer>();
 287             for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorPostorder(); it.hasNext(); ) {
 288                 final PhylogenyNode n = it.next();
 289                 final Set<String> gained_dc = n.getNodeData().getBinaryCharacters().getGainedCharacters();
 290                 for( final String dc : gained_dc ) {
 291                     if ( dc_gain_counts.containsKey( dc ) ) {
 292                         dc_gain_counts.put( dc, dc_gain_counts.get( dc ) + 1 );
 293                     }
 294                     else {
 295                         dc_gain_counts.put( dc, 1 );
 296                     }
 297                 }
 298             }
 299             final SortedMap<Integer, Integer> histogram = new TreeMap<Integer, Integer>();
 300             final SortedMap<Integer, StringBuilder> domain_lists = new TreeMap<Integer, StringBuilder>();
 301             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_protein_length_stats = new TreeMap<Integer, DescriptiveStatistics>();
 302             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_number_stats = new TreeMap<Integer, DescriptiveStatistics>();
 303             final SortedMap<Integer, DescriptiveStatistics> dc_reapp_counts_to_domain_lengths_stats = new TreeMap<Integer, DescriptiveStatistics>();
 304             final SortedMap<Integer, PriorityQueue<String>> domain_lists_go = new TreeMap<Integer, PriorityQueue<String>>();
 305             final SortedMap<Integer, SortedSet<String>> domain_lists_go_unique = new TreeMap<Integer, SortedSet<String>>();
 306             final Set<String> dcs = dc_gain_counts.keySet();
 307             final SortedSet<String> more_than_once = new TreeSet<String>();
 308             final DescriptiveStatistics gained_once_lengths_stats = new BasicDescriptiveStatistics();
 309             final DescriptiveStatistics gained_once_domain_count_stats = new BasicDescriptiveStatistics();
 310             final DescriptiveStatistics gained_multiple_times_lengths_stats = new BasicDescriptiveStatistics();
 311             final DescriptiveStatistics gained_multiple_times_domain_count_stats = new BasicDescriptiveStatistics();
 312             long gained_multiple_times_domain_length_sum = 0;
 313             long gained_once_domain_length_sum = 0;
 314             long gained_multiple_times_domain_length_count = 0;
 315             long gained_once_domain_length_count = 0;
 316             for( final String dc : dcs ) {
 317                 final int count = dc_gain_counts.get( dc );
 318                 if ( histogram.containsKey( count ) ) {
 319                     histogram.put( count, histogram.get( count ) + 1 );
 320                     domain_lists.get( count ).append( ", " + dc );
 321                     domain_lists_go.get( count ).addAll( splitDomainCombination( dc ) );
 322                     domain_lists_go_unique.get( count ).addAll( splitDomainCombination( dc ) );
 323                 }
 324                 else {
 325                     histogram.put( count, 1 );
 326                     domain_lists.put( count, new StringBuilder( dc ) );
 327                     final PriorityQueue<String> q = new PriorityQueue<String>();
 328                     q.addAll( splitDomainCombination( dc ) );
 329                     domain_lists_go.put( count, q );
 330                     final SortedSet<String> set = new TreeSet<String>();
 331                     set.addAll( splitDomainCombination( dc ) );
 332                     domain_lists_go_unique.put( count, set );
 333                 }
 334                 if ( protein_length_stats_by_dc != null ) {
 335                     if ( !dc_reapp_counts_to_protein_length_stats.containsKey( count ) ) {
 336                         dc_reapp_counts_to_protein_length_stats.put( count, new BasicDescriptiveStatistics() );
 337                     }
 338                     dc_reapp_counts_to_protein_length_stats.get( count ).addValue( protein_length_stats_by_dc.get( dc )
 339                             .arithmeticMean() );
 340                 }
 341                 if ( domain_number_stats_by_dc != null ) {
 342                     if ( !dc_reapp_counts_to_domain_number_stats.containsKey( count ) ) {
 343                         dc_reapp_counts_to_domain_number_stats.put( count, new BasicDescriptiveStatistics() );
 344                     }
 345                     dc_reapp_counts_to_domain_number_stats.get( count ).addValue( domain_number_stats_by_dc.get( dc )
 346                             .arithmeticMean() );
 347                 }
 348                 if ( domain_length_stats_by_domain != null ) {
 349                     if ( !dc_reapp_counts_to_domain_lengths_stats.containsKey( count ) ) {
 350                         dc_reapp_counts_to_domain_lengths_stats.put( count, new BasicDescriptiveStatistics() );
 351                     }
 352                     final String[] ds = dc.split( "=" );
 353                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
 354                             .get( ds[ 0 ] ).arithmeticMean() );
 355                     dc_reapp_counts_to_domain_lengths_stats.get( count ).addValue( domain_length_stats_by_domain
 356                             .get( ds[ 1 ] ).arithmeticMean() );
 357                 }
 358                 if ( count > 1 ) {
 359                     more_than_once.add( dc );
 360                     if ( protein_length_stats_by_dc != null ) {
 361                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
 362                         for( final double element : s.getData() ) {
 363                             gained_multiple_times_lengths_stats.addValue( element );
 364                         }
 365                     }
 366                     if ( domain_number_stats_by_dc != null ) {
 367                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
 368                         for( final double element : s.getData() ) {
 369                             gained_multiple_times_domain_count_stats.addValue( element );
 370                         }
 371                     }
 372                     if ( domain_length_stats_by_domain != null ) {
 373                         final String[] ds = dc.split( "=" );
 374                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
 375                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
 376                         for( final double element : s0.getData() ) {
 377                             gained_multiple_times_domain_length_sum += element;
 378                             ++gained_multiple_times_domain_length_count;
 379                         }
 380                         for( final double element : s1.getData() ) {
 381                             gained_multiple_times_domain_length_sum += element;
 382                             ++gained_multiple_times_domain_length_count;
 383                         }
 384                     }
 385                 }
 386                 else {
 387                     if ( protein_length_stats_by_dc != null ) {
 388                         final DescriptiveStatistics s = protein_length_stats_by_dc.get( dc );
 389                         for( final double element : s.getData() ) {
 390                             gained_once_lengths_stats.addValue( element );
 391                         }
 392                     }
 393                     if ( domain_number_stats_by_dc != null ) {
 394                         final DescriptiveStatistics s = domain_number_stats_by_dc.get( dc );
 395                         for( final double element : s.getData() ) {
 396                             gained_once_domain_count_stats.addValue( element );
 397                         }
 398                     }
 399                     if ( domain_length_stats_by_domain != null ) {
 400                         final String[] ds = dc.split( "=" );
 401                         final DescriptiveStatistics s0 = domain_length_stats_by_domain.get( ds[ 0 ] );
 402                         final DescriptiveStatistics s1 = domain_length_stats_by_domain.get( ds[ 1 ] );
 403                         for( final double element : s0.getData() ) {
 404                             gained_once_domain_length_sum += element;
 405                             ++gained_once_domain_length_count;
 406                         }
 407                         for( final double element : s1.getData() ) {
 408                             gained_once_domain_length_sum += element;
 409                             ++gained_once_domain_length_count;
 410                         }
 411                     }
 412                 }
 413             }
 414             final Set<Integer> histogram_keys = histogram.keySet();
 415             for( final Integer histogram_key : histogram_keys ) {
 416                 final int count = histogram.get( histogram_key );
 417                 final StringBuilder dc = domain_lists.get( histogram_key );
 418                 out_counts.write( histogram_key + "\t" + count + ForesterUtil.LINE_SEPARATOR );
 419                 out_dc.write( histogram_key + "\t" + dc + ForesterUtil.LINE_SEPARATOR );
 420                 out_dc_for_go_mapping.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 421                 final Object[] sorted = domain_lists_go.get( histogram_key ).toArray();
 422                 Arrays.sort( sorted );
 423                 for( final Object domain : sorted ) {
 424                     out_dc_for_go_mapping.write( domain + ForesterUtil.LINE_SEPARATOR );
 425                 }
 426                 out_dc_for_go_mapping_unique.write( "#" + histogram_key + ForesterUtil.LINE_SEPARATOR );
 427                 for( final String domain : domain_lists_go_unique.get( histogram_key ) ) {
 428                     out_dc_for_go_mapping_unique.write( domain + ForesterUtil.LINE_SEPARATOR );
 429                 }
 430             }
 431             out_counts.close();
 432             out_dc.close();
 433             out_dc_for_go_mapping.close();
 434             out_dc_for_go_mapping_unique.close();
 435             final SortedMap<String, Integer> lca_rank_counts = new TreeMap<String, Integer>();
 436             final SortedMap<String, Integer> lca_ancestor_species_counts = new TreeMap<String, Integer>();
 437             for( final String dc : more_than_once ) {
 438                 final List<PhylogenyNode> nodes = new ArrayList<PhylogenyNode>();
 439                 for( final PhylogenyNodeIterator it = local_phylogeny_l.iteratorExternalForward(); it.hasNext(); ) {
 440                     final PhylogenyNode n = it.next();
 441                     if ( n.getNodeData().getBinaryCharacters().getGainedCharacters().contains( dc ) ) {
 442                         nodes.add( n );
 443                     }
 444                 }
 445                 for( int i = 0; i < ( nodes.size() - 1 ); ++i ) {
 446                     for( int j = i + 1; j < nodes.size(); ++j ) {
 447                         final PhylogenyNode lca = PhylogenyMethods.calculateLCA( nodes.get( i ), nodes.get( j ) );
 448                         String rank = "unknown";
 449                         if ( lca.getNodeData().isHasTaxonomy()
 450                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getRank() ) ) {
 451                             rank = lca.getNodeData().getTaxonomy().getRank();
 452                         }
 453                         addToCountMap( lca_rank_counts, rank );
 454                         String lca_species;
 455                         if ( lca.getNodeData().isHasTaxonomy()
 456                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getScientificName() ) ) {
 457                             lca_species = lca.getNodeData().getTaxonomy().getScientificName();
 458                         }
 459                         else if ( lca.getNodeData().isHasTaxonomy()
 460                                 && !ForesterUtil.isEmpty( lca.getNodeData().getTaxonomy().getCommonName() ) ) {
 461                             lca_species = lca.getNodeData().getTaxonomy().getCommonName();
 462                         }
 463                         else {
 464                             lca_species = lca.getName();
 465                         }
 466                         addToCountMap( lca_ancestor_species_counts, lca_species );
 467                     }
 468                 }
 469             }
 470             final BufferedWriter out_for_rank_counts = new BufferedWriter( new FileWriter( outfilename_for_rank_counts ) );
 471             final BufferedWriter out_for_ancestor_species_counts = new BufferedWriter( new FileWriter( outfilename_for_ancestor_species_counts ) );
 472             ForesterUtil.map2writer( out_for_rank_counts, lca_rank_counts, "\t", ForesterUtil.LINE_SEPARATOR );
 473             ForesterUtil.map2writer( out_for_ancestor_species_counts,
 474                                      lca_ancestor_species_counts,
 475                                      "\t",
 476                                      ForesterUtil.LINE_SEPARATOR );
 477             out_for_rank_counts.close();
 478             out_for_ancestor_species_counts.close();
 479             if ( !ForesterUtil.isEmpty( outfilename_for_protein_stats )
 480                     && ( ( domain_length_stats_by_domain != null ) || ( protein_length_stats_by_dc != null ) || ( domain_number_stats_by_dc != null ) ) ) {
 481                 final BufferedWriter w = new BufferedWriter( new FileWriter( outfilename_for_protein_stats ) );
 482                 w.write( "Domain Lengths: " );
 483                 w.write( "\n" );
 484                 if ( domain_length_stats_by_domain != null ) {
 485                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_lengths_stats
 486                             .entrySet() ) {
 487                         w.write( entry.getKey().toString() );
 488                         w.write( "\t" + entry.getValue().arithmeticMean() );
 489                         w.write( "\t" + entry.getValue().median() );
 490                         w.write( "\n" );
 491                     }
 492                 }
 493                 w.flush();
 494                 w.write( "\n" );
 495                 w.write( "\n" );
 496                 w.write( "Protein Lengths: " );
 497                 w.write( "\n" );
 498                 if ( protein_length_stats_by_dc != null ) {
 499                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_protein_length_stats
 500                             .entrySet() ) {
 501                         w.write( entry.getKey().toString() );
 502                         w.write( "\t" + entry.getValue().arithmeticMean() );
 503                         w.write( "\t" + entry.getValue().median() );
 504                         w.write( "\n" );
 505                     }
 506                 }
 507                 w.flush();
 508                 w.write( "\n" );
 509                 w.write( "\n" );
 510                 w.write( "Number of domains: " );
 511                 w.write( "\n" );
 512                 if ( domain_number_stats_by_dc != null ) {
 513                     for( final Entry<Integer, DescriptiveStatistics> entry : dc_reapp_counts_to_domain_number_stats
 514                             .entrySet() ) {
 515                         w.write( entry.getKey().toString() );
 516                         w.write( "\t" + entry.getValue().arithmeticMean() );
 517                         w.write( "\t" + entry.getValue().median() );
 518                         w.write( "\n" );
 519                     }
 520                 }
 521                 w.flush();
 522                 w.write( "\n" );
 523                 w.write( "\n" );
 524                 w.write( "Gained once, domain lengths:" );
 525                 w.write( "\n" );
 526                 w.write( "N: " + gained_once_domain_length_count );
 527                 w.write( "\n" );
 528                 w.write( "Avg: " + ( ( double ) gained_once_domain_length_sum / gained_once_domain_length_count ) );
 529                 w.write( "\n" );
 530                 w.write( "\n" );
 531                 w.write( "Gained multiple times, domain lengths:" );
 532                 w.write( "\n" );
 533                 w.write( "N: " + gained_multiple_times_domain_length_count );
 534                 w.write( "\n" );
 535                 w.write( "Avg: "
 536                         + ( ( double ) gained_multiple_times_domain_length_sum / gained_multiple_times_domain_length_count ) );
 537                 w.write( "\n" );
 538                 w.write( "\n" );
 539                 w.write( "\n" );
 540                 w.write( "\n" );
 541                 w.write( "Gained once, protein lengths:" );
 542                 w.write( "\n" );
 543                 w.write( gained_once_lengths_stats.toString() );
 544                 w.write( "\n" );
 545                 w.write( "\n" );
 546                 w.write( "Gained once, domain counts:" );
 547                 w.write( "\n" );
 548                 w.write( gained_once_domain_count_stats.toString() );
 549                 w.write( "\n" );
 550                 w.write( "\n" );
 551                 w.write( "Gained multiple times, protein lengths:" );
 552                 w.write( "\n" );
 553                 w.write( gained_multiple_times_lengths_stats.toString() );
 554                 w.write( "\n" );
 555                 w.write( "\n" );
 556                 w.write( "Gained multiple times, domain counts:" );
 557                 w.write( "\n" );
 558                 w.write( gained_multiple_times_domain_count_stats.toString() );
 559                 w.flush();
 560                 w.close();
 561             }
 562         }
 563         catch ( final IOException e ) {
 564             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
 565         }
 566         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch counts to ["
 567                 + outfilename_for_counts + "]" );
 568         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote independent domain combination gains fitch lists to ["
 569                 + outfilename_for_dc + "]" );
 570         ForesterUtil.programMessage( surfacing.PRG_NAME,
 571                                      "Wrote independent domain combination gains fitch lists to (for GO mapping) ["
 572                                              + outfilename_for_dc_for_go_mapping + "]" );
 573         ForesterUtil.programMessage( surfacing.PRG_NAME,
 574                                      "Wrote independent domain combination gains fitch lists to (for GO mapping, unique) ["
 575                                              + outfilename_for_dc_for_go_mapping_unique + "]" );
 576     }
 577
 578     private final static void addToCountMap( final Map<String, Integer> map, final String s ) {
 579         if ( map.containsKey( s ) ) {
 580             map.put( s, map.get( s ) + 1 );
 581         }
 582         else {
 583             map.put( s, 1 );
 584         }
 585     }
 586
 587     public static int calculateOverlap( final Domain domain, final List<Boolean> covered_positions ) {
 588         int overlap_count = 0;
 589         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
 590             if ( ( i < covered_positions.size() ) && ( covered_positions.get( i ) == true ) ) {
 591                 ++overlap_count;
 592             }
 593         }
 594         return overlap_count;
 595     }
 596
 597     public static void checkForOutputFileWriteability( final File outfile ) {
 598         final String error = ForesterUtil.isWritableFile( outfile );
 599         if ( !ForesterUtil.isEmpty( error ) ) {
 600             ForesterUtil.fatalError( surfacing.PRG_NAME, error );
 601         }
 602     }
 603
 604     private static SortedSet<String> collectAllDomainsChangedOnSubtree( final PhylogenyNode subtree_root,
 605                                                                         final boolean get_gains ) {
 606         final SortedSet<String> domains = new TreeSet<String>();
 607         for( final PhylogenyNode descendant : PhylogenyMethods.getAllDescendants( subtree_root ) ) {
 608             final BinaryCharacters chars = descendant.getNodeData().getBinaryCharacters();
 609             if ( get_gains ) {
 610                 domains.addAll( chars.getGainedCharacters() );
 611             }
 612             else {
 613                 domains.addAll( chars.getLostCharacters() );
 614             }
 615         }
 616         return domains;
 617     }
 618
 619     public static void collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
 620                                                                                            final BinaryDomainCombination.DomainCombinationType dc_type,
 621                                                                                            final List<BinaryDomainCombination> all_binary_domains_combination_gained,
 622                                                                                            final boolean get_gains ) {
 623         final SortedSet<String> sorted_ids = new TreeSet<String>();
 624         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
 625             sorted_ids.add( matrix.getIdentifier( i ) );
 626         }
 627         for( final String id : sorted_ids ) {
 628             for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
 629                 if ( ( get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) )
 630                         || ( !get_gains && ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.LOSS ) ) ) {
 631                     if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED_ADJACTANT ) {
 632                         all_binary_domains_combination_gained.add( AdjactantDirectedBinaryDomainCombination
 633                                 .createInstance( matrix.getCharacter( c ) ) );
 634                     }
 635                     else if ( dc_type == BinaryDomainCombination.DomainCombinationType.DIRECTED ) {
 636                         all_binary_domains_combination_gained.add( DirectedBinaryDomainCombination
 637                                 .createInstance( matrix.getCharacter( c ) ) );
 638                     }
 639                     else {
 640                         all_binary_domains_combination_gained.add( BasicBinaryDomainCombination.createInstance( matrix
 641                                 .getCharacter( c ) ) );
 642                     }
 643                 }
 644             }
 645         }
 646     }
 647
 648     private static File createBaseDirForPerNodeDomainFiles( final String base_dir,
 649                                                             final boolean domain_combinations,
 650                                                             final CharacterStateMatrix.GainLossStates state,
 651                                                             final String outfile ) {
 652         File per_node_go_mapped_domain_gain_loss_files_base_dir = new File( new File( outfile ).getParent()
 653                 + ForesterUtil.FILE_SEPARATOR + base_dir );
 654         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 655             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 656         }
 657         if ( domain_combinations ) {
 658             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 659                     + ForesterUtil.FILE_SEPARATOR + "DC" );
 660         }
 661         else {
 662             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 663                     + ForesterUtil.FILE_SEPARATOR + "DOMAINS" );
 664         }
 665         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 666             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 667         }
 668         if ( state == GainLossStates.GAIN ) {
 669             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 670                     + ForesterUtil.FILE_SEPARATOR + "GAINS" );
 671         }
 672         else if ( state == GainLossStates.LOSS ) {
 673             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 674                     + ForesterUtil.FILE_SEPARATOR + "LOSSES" );
 675         }
 676         else {
 677             per_node_go_mapped_domain_gain_loss_files_base_dir = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
 678                     + ForesterUtil.FILE_SEPARATOR + "PRESENT" );
 679         }
 680         if ( !per_node_go_mapped_domain_gain_loss_files_base_dir.exists() ) {
 681             per_node_go_mapped_domain_gain_loss_files_base_dir.mkdir();
 682         }
 683         return per_node_go_mapped_domain_gain_loss_files_base_dir;
 684     }
 685
 686     public static Map<DomainId, List<GoId>> createDomainIdToGoIdMap( final List<PfamToGoMapping> pfam_to_go_mappings ) {
 687         final Map<DomainId, List<GoId>> domain_id_to_go_ids_map = new HashMap<DomainId, List<GoId>>( pfam_to_go_mappings
 688                 .size() );
 689         for( final PfamToGoMapping pfam_to_go : pfam_to_go_mappings ) {
 690             if ( !domain_id_to_go_ids_map.containsKey( pfam_to_go.getKey() ) ) {
 691                 domain_id_to_go_ids_map.put( pfam_to_go.getKey(), new ArrayList<GoId>() );
 692             }
 693             domain_id_to_go_ids_map.get( pfam_to_go.getKey() ).add( pfam_to_go.getValue() );
 694         }
 695         return domain_id_to_go_ids_map;
 696     }
 697
 698     public static Map<DomainId, Set<String>> createDomainIdToSecondaryFeaturesMap( final File secondary_features_map_file )
 699             throws IOException {
 700         final BasicTable<String> primary_table = BasicTableParser.parse( secondary_features_map_file, '\t' );
 701         final Map<DomainId, Set<String>> map = new TreeMap<DomainId, Set<String>>();
 702         for( int r = 0; r < primary_table.getNumberOfRows(); ++r ) {
 703             final DomainId domain_id = new DomainId( primary_table.getValue( 0, r ) );
 704             if ( !map.containsKey( domain_id ) ) {
 705                 map.put( domain_id, new HashSet<String>() );
 706             }
 707             map.get( domain_id ).add( primary_table.getValue( 1, r ) );
 708         }
 709         return map;
 710     }
 711
 712     public static Phylogeny createNjTreeBasedOnMatrixToFile( final File nj_tree_outfile, final DistanceMatrix distance ) {
 713         checkForOutputFileWriteability( nj_tree_outfile );
 714         final NeighborJoining nj = NeighborJoining.createInstance();
 715         final Phylogeny phylogeny = nj.execute( ( BasicSymmetricalDistanceMatrix ) distance );
 716         phylogeny.setName( nj_tree_outfile.getName() );
 717         writePhylogenyToFile( phylogeny, nj_tree_outfile.toString() );
 718         return phylogeny;
 719     }
 720
 721     private static SortedSet<BinaryDomainCombination> createSetOfAllBinaryDomainCombinationsPerGenome( final GenomeWideCombinableDomains gwcd ) {
 722         final SortedMap<DomainId, CombinableDomains> cds = gwcd.getAllCombinableDomainsIds();
 723         final SortedSet<BinaryDomainCombination> binary_combinations = new TreeSet<BinaryDomainCombination>();
 724         for( final DomainId domain_id : cds.keySet() ) {
 725             final CombinableDomains cd = cds.get( domain_id );
 726             binary_combinations.addAll( cd.toBinaryDomainCombinations() );
 727         }
 728         return binary_combinations;
 729     }
 730
 731     public static void decoratePrintableDomainSimilarities( final SortedSet<DomainSimilarity> domain_similarities,
 732                                                             final Detailedness detailedness,
 733                                                             final GoAnnotationOutput go_annotation_output,
 734                                                             final Map<GoId, GoTerm> go_id_to_term_map,
 735                                                             final GoNameSpace go_namespace_limit ) {
 736         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || go_id_to_term_map.isEmpty() ) ) {
 737             throw new IllegalArgumentException( "attempt to use a GO namespace limit without a GO id to term map" );
 738         }
 739         for( final DomainSimilarity domain_similarity : domain_similarities ) {
 740             if ( domain_similarity instanceof PrintableDomainSimilarity ) {
 741                 final PrintableDomainSimilarity printable_domain_similarity = ( PrintableDomainSimilarity ) domain_similarity;
 742                 printable_domain_similarity.setDetailedness( detailedness );
 743                 printable_domain_similarity.setGoAnnotationOutput( go_annotation_output );
 744                 printable_domain_similarity.setGoIdToTermMap( go_id_to_term_map );
 745                 printable_domain_similarity.setGoNamespaceLimit( go_namespace_limit );
 746             }
 747         }
 748     }
 749
 750     public static void executeDomainLengthAnalysis( final String[][] input_file_properties,
 751                                                     final int number_of_genomes,
 752                                                     final DomainLengthsTable domain_lengths_table,
 753                                                     final File outfile ) throws IOException {
 754         final DecimalFormat df = new DecimalFormat( "#.00" );
 755         checkForOutputFileWriteability( outfile );
 756         final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
 757         out.write( "MEAN BASED STATISTICS PER SPECIES" );
 758         out.write( ForesterUtil.LINE_SEPARATOR );
 759         out.write( domain_lengths_table.createMeanBasedStatisticsPerSpeciesTable().toString() );
 760         out.write( ForesterUtil.LINE_SEPARATOR );
 761         out.write( ForesterUtil.LINE_SEPARATOR );
 762         final List<DomainLengths> domain_lengths_list = domain_lengths_table.getDomainLengthsList();
 763         out.write( "OUTLIER SPECIES PER DOMAIN (Z>=1.5)" );
 764         out.write( ForesterUtil.LINE_SEPARATOR );
 765         for( final DomainLengths domain_lengths : domain_lengths_list ) {
 766             final List<Species> species_list = domain_lengths.getMeanBasedOutlierSpecies( 1.5 );
 767             if ( species_list.size() > 0 ) {
 768                 out.write( domain_lengths.getDomainId() + "\t" );
 769                 for( final Species species : species_list ) {
 770                     out.write( species + "\t" );
 771                 }
 772                 out.write( ForesterUtil.LINE_SEPARATOR );
 773                 // DescriptiveStatistics stats_for_domain = domain_lengths
 774                 //         .calculateMeanBasedStatistics();
 775                 //AsciiHistogram histo = new AsciiHistogram( stats_for_domain );
 776                 //System.out.println( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 777             }
 778         }
 779         out.write( ForesterUtil.LINE_SEPARATOR );
 780         out.write( ForesterUtil.LINE_SEPARATOR );
 781         out.write( "OUTLIER SPECIES (Z 1.0)" );
 782         out.write( ForesterUtil.LINE_SEPARATOR );
 783         final DescriptiveStatistics stats_for_all_species = domain_lengths_table
 784                 .calculateMeanBasedStatisticsForAllSpecies();
 785         out.write( stats_for_all_species.asSummary() );
 786         out.write( ForesterUtil.LINE_SEPARATOR );
 787         final AsciiHistogram histo = new AsciiHistogram( stats_for_all_species );
 788         out.write( histo.toStringBuffer( 40, '=', 60, 4 ).toString() );
 789         out.write( ForesterUtil.LINE_SEPARATOR );
 790         final double population_sd = stats_for_all_species.sampleStandardDeviation();
 791         final double population_mean = stats_for_all_species.arithmeticMean();
 792         for( final Species species : domain_lengths_table.getSpecies() ) {
 793             final double x = domain_lengths_table.calculateMeanBasedStatisticsForSpecies( species ).arithmeticMean();
 794             final double z = ( x - population_mean ) / population_sd;
 795             out.write( species + "\t" + z );
 796             out.write( ForesterUtil.LINE_SEPARATOR );
 797         }
 798         out.write( ForesterUtil.LINE_SEPARATOR );
 799         for( final Species species : domain_lengths_table.getSpecies() ) {
 800             final DescriptiveStatistics stats_for_species = domain_lengths_table
 801                     .calculateMeanBasedStatisticsForSpecies( species );
 802             final double x = stats_for_species.arithmeticMean();
 803             final double z = ( x - population_mean ) / population_sd;
 804             if ( ( z <= -1.0 ) || ( z >= 1.0 ) ) {
 805                 out.write( species + "\t" + df.format( z ) + "\t" + stats_for_species.asSummary() );
 806                 out.write( ForesterUtil.LINE_SEPARATOR );
 807             }
 808         }
 809         out.close();
 810         //        final List<HistogramData> histogram_datas = new ArrayList<HistogramData>();
 811         //        for( int i = 0; i < number_of_genomes; ++i ) {
 812         //            final Species species = new BasicSpecies( input_file_properties[ i ][ 0 ] );
 813         //            histogram_datas
 814         //                    .add( new HistogramData( species.toString(), domain_lengths_table
 815         //                            .calculateMeanBasedStatisticsForSpecies( species )
 816         //                            .getDataAsDoubleArray(), 5, 600, null, 60 ) );
 817         //        }
 818         //        final HistogramsFrame hf = new HistogramsFrame( histogram_datas );
 819         //        hf.setVisible( true );
 820         System.gc();
 821     }
 822
 823     /**
 824      *
 825      * @param all_binary_domains_combination_lost_fitch
 826      * @param consider_directedness_and_adjacency_for_bin_combinations
 827      * @param all_binary_domains_combination_gained if null ignored, otherwise this is to list all binary domain combinations
 828      * which were gained under unweighted (Fitch) parsimony.
 829      */
 830     public static void executeParsimonyAnalysis( final long random_number_seed_for_fitch_parsimony,
 831                                                  final boolean radomize_fitch_parsimony,
 832                                                  final String outfile_name,
 833                                                  final DomainParsimonyCalculator domain_parsimony,
 834                                                  final Phylogeny phylogeny,
 835                                                  final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
 836                                                  final Map<GoId, GoTerm> go_id_to_term_map,
 837                                                  final GoNameSpace go_namespace_limit,
 838                                                  final String parameters_str,
 839                                                  final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
 840                                                  final SortedSet<DomainId> positive_filter,
 841                                                  final boolean output_binary_domain_combinations_for_graphs,
 842                                                  final List<BinaryDomainCombination> all_binary_domains_combination_gained_fitch,
 843                                                  final List<BinaryDomainCombination> all_binary_domains_combination_lost_fitch,
 844                                                  final BinaryDomainCombination.DomainCombinationType dc_type,
 845                                                  final Map<String, DescriptiveStatistics> protein_length_stats_by_dc,
 846                                                  final Map<String, DescriptiveStatistics> domain_number_stats_by_dc,
 847                                                  final Map<String, DescriptiveStatistics> domain_length_stats_by_domain ) {
 848         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
 849         final String date_time = ForesterUtil.getCurrentDateTime();
 850         final SortedSet<String> all_pfams_encountered = new TreeSet<String>();
 851         final SortedSet<String> all_pfams_gained_as_domains = new TreeSet<String>();
 852         final SortedSet<String> all_pfams_lost_as_domains = new TreeSet<String>();
 853         final SortedSet<String> all_pfams_gained_as_dom_combinations = new TreeSet<String>();
 854         final SortedSet<String> all_pfams_lost_as_dom_combinations = new TreeSet<String>();
 855         writeToNexus( outfile_name, domain_parsimony, phylogeny );
 856         // DOLLO DOMAINS
 857         // -------------
 858         Phylogeny local_phylogeny_l = phylogeny.copy();
 859         if ( ( positive_filter != null ) && ( positive_filter.size() > 0 ) ) {
 860             domain_parsimony.executeDolloParsimonyOnDomainPresence( positive_filter );
 861         }
 862         else {
 863             domain_parsimony.executeDolloParsimonyOnDomainPresence();
 864         }
 865         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 866                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 867         SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 868                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_DOMAINS, Format.FORESTER );
 869         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 870                                                            CharacterStateMatrix.GainLossStates.GAIN,
 871                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_D,
 872                                                            sep,
 873                                                            ForesterUtil.LINE_SEPARATOR,
 874                                                            null );
 875         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 876                                                            CharacterStateMatrix.GainLossStates.LOSS,
 877                                                            outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_D,
 878                                                            sep,
 879                                                            ForesterUtil.LINE_SEPARATOR,
 880                                                            null );
 881         SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 882                 + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_D, sep, ForesterUtil.LINE_SEPARATOR, null );
 883         //HTML:
 884         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 885                                        go_id_to_term_map,
 886                                        go_namespace_limit,
 887                                        false,
 888                                        domain_parsimony.getGainLossMatrix(),
 889                                        CharacterStateMatrix.GainLossStates.GAIN,
 890                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_HTML_D,
 891                                        sep,
 892                                        ForesterUtil.LINE_SEPARATOR,
 893                                        "Dollo Parsimony | Gains | Domains",
 894                                        "+",
 895                                        domain_id_to_secondary_features_maps,
 896                                        all_pfams_encountered,
 897                                        all_pfams_gained_as_domains,
 898                                        "_dollo_gains_d" );
 899         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 900                                        go_id_to_term_map,
 901                                        go_namespace_limit,
 902                                        false,
 903                                        domain_parsimony.getGainLossMatrix(),
 904                                        CharacterStateMatrix.GainLossStates.LOSS,
 905                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_HTML_D,
 906                                        sep,
 907                                        ForesterUtil.LINE_SEPARATOR,
 908                                        "Dollo Parsimony | Losses | Domains",
 909                                        "-",
 910                                        domain_id_to_secondary_features_maps,
 911                                        all_pfams_encountered,
 912                                        all_pfams_lost_as_domains,
 913                                        "_dollo_losses_d" );
 914         writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
 915                                        go_id_to_term_map,
 916                                        go_namespace_limit,
 917                                        false,
 918                                        domain_parsimony.getGainLossMatrix(),
 919                                        null,
 920                                        outfile_name + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_HTML_D,
 921                                        sep,
 922                                        ForesterUtil.LINE_SEPARATOR,
 923                                        "Dollo Parsimony | Present | Domains",
 924                                        "",
 925                                        domain_id_to_secondary_features_maps,
 926                                        all_pfams_encountered,
 927                                        null,
 928                                        "_dollo_present_d" );
 929         preparePhylogeny( local_phylogeny_l,
 930                           domain_parsimony,
 931                           date_time,
 932                           "Dollo parsimony on domain presence/absence",
 933                           "dollo_on_domains_" + outfile_name,
 934                           parameters_str );
 935         SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
 936                 + surfacing.DOMAINS_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
 937         try {
 938             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, true, outfile_name, "_dollo_all_gains_d" );
 939             writeAllDomainsChangedOnAllSubtrees( local_phylogeny_l, false, outfile_name, "_dollo_all_losses_d" );
 940         }
 941         catch ( final IOException e ) {
 942             e.printStackTrace();
 943             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
 944         }
 945         if ( domain_parsimony.calculateNumberOfBinaryDomainCombination() > 0 ) {
 946             // FITCH DOMAIN COMBINATIONS
 947             // -------------------------
 948             local_phylogeny_l = phylogeny.copy();
 949             String randomization = "no";
 950             if ( radomize_fitch_parsimony ) {
 951                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( random_number_seed_for_fitch_parsimony );
 952                 randomization = "yes, seed = " + random_number_seed_for_fitch_parsimony;
 953             }
 954             else {
 955                 domain_parsimony.executeFitchParsimonyOnBinaryDomainCombintion( USE_LAST );
 956             }
 957             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossMatrix(), outfile_name
 958                     + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 959             SurfacingUtil.writeMatrixToFile( domain_parsimony.getGainLossCountsMatrix(), outfile_name
 960                     + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_FITCH_BINARY_COMBINATIONS, Format.FORESTER );
 961             SurfacingUtil
 962                     .writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 963                                                           CharacterStateMatrix.GainLossStates.GAIN,
 964                                                           outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_BC,
 965                                                           sep,
 966                                                           ForesterUtil.LINE_SEPARATOR,
 967                                                           null );
 968             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 969                                                                CharacterStateMatrix.GainLossStates.LOSS,
 970                                                                outfile_name
 971                                                                        + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_BC,
 972                                                                sep,
 973                                                                ForesterUtil.LINE_SEPARATOR,
 974                                                                null );
 975             SurfacingUtil.writeBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(), null, outfile_name
 976                     + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC, sep, ForesterUtil.LINE_SEPARATOR, null );
 977             if ( all_binary_domains_combination_gained_fitch != null ) {
 978                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 979                                                                                     dc_type,
 980                                                                                     all_binary_domains_combination_gained_fitch,
 981                                                                                     true );
 982             }
 983             if ( all_binary_domains_combination_lost_fitch != null ) {
 984                 collectChangedDomainCombinationsFromBinaryStatesMatrixAsListToFile( domain_parsimony.getGainLossMatrix(),
 985                                                                                     dc_type,
 986                                                                                     all_binary_domains_combination_lost_fitch,
 987                                                                                     false );
 988             }
 989             if ( output_binary_domain_combinations_for_graphs ) {
 990                 SurfacingUtil
 991                         .writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( domain_parsimony
 992                                                                                                            .getGainLossMatrix(),
 993                                                                                                    null,
 994                                                                                                    outfile_name
 995                                                                                                            + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_BC_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS,
 996                                                                                                    sep,
 997                                                                                                    ForesterUtil.LINE_SEPARATOR,
 998                                                                                                    BinaryDomainCombination.OutputFormat.DOT );
 999             }
1000             // HTML:
1001             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
1002                                            go_id_to_term_map,
1003                                            go_namespace_limit,
1004                                            true,
1005                                            domain_parsimony.getGainLossMatrix(),
1006                                            CharacterStateMatrix.GainLossStates.GAIN,
1007                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_GAINS_HTML_BC,
1008                                            sep,
1009                                            ForesterUtil.LINE_SEPARATOR,
1010                                            "Fitch Parsimony | Gains | Domain Combinations",
1011                                            "+",
1012                                            null,
1013                                            all_pfams_encountered,
1014                                            all_pfams_gained_as_dom_combinations,
1015                                            "_fitch_gains_dc" );
1016             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
1017                                            go_id_to_term_map,
1018                                            go_namespace_limit,
1019                                            true,
1020                                            domain_parsimony.getGainLossMatrix(),
1021                                            CharacterStateMatrix.GainLossStates.LOSS,
1022                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_LOSSES_HTML_BC,
1023                                            sep,
1024                                            ForesterUtil.LINE_SEPARATOR,
1025                                            "Fitch Parsimony | Losses | Domain Combinations",
1026                                            "-",
1027                                            null,
1028                                            all_pfams_encountered,
1029                                            all_pfams_lost_as_dom_combinations,
1030                                            "_fitch_losses_dc" );
1031             writeBinaryStatesMatrixToList( domain_id_to_go_ids_map,
1032                                            go_id_to_term_map,
1033                                            go_namespace_limit,
1034                                            true,
1035                                            domain_parsimony.getGainLossMatrix(),
1036                                            null,
1037                                            outfile_name + surfacing.PARSIMONY_OUTPUT_FITCH_PRESENT_HTML_BC,
1038                                            sep,
1039                                            ForesterUtil.LINE_SEPARATOR,
1040                                            "Fitch Parsimony | Present | Domain Combinations",
1041                                            "",
1042                                            null,
1043                                            all_pfams_encountered,
1044                                            null,
1045                                            "_fitch_present_dc" );
1046             writeAllEncounteredPfamsToFile( domain_id_to_go_ids_map,
1047                                             go_id_to_term_map,
1048                                             outfile_name,
1049                                             all_pfams_encountered );
1050             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DOMAINS_SUFFIX, all_pfams_gained_as_domains );
1051             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DOMAINS_SUFFIX, all_pfams_lost_as_domains );
1052             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_GAINED_AS_DC_SUFFIX,
1053                               all_pfams_gained_as_dom_combinations );
1054             writePfamsToFile( outfile_name + surfacing.ALL_PFAMS_LOST_AS_DC_SUFFIX, all_pfams_lost_as_dom_combinations );
1055             preparePhylogeny( local_phylogeny_l,
1056                               domain_parsimony,
1057                               date_time,
1058                               "Fitch parsimony on binary domain combination presence/absence randomization: "
1059                                       + randomization,
1060                               "fitch_on_binary_domain_combinations_" + outfile_name,
1061                               parameters_str );
1062             SurfacingUtil.writePhylogenyToFile( local_phylogeny_l, outfile_name
1063                     + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH );
1064             calculateIndependentDomainCombinationGains( local_phylogeny_l,
1065                                                         outfile_name
1066                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_OUTPUT_SUFFIX,
1067                                                         outfile_name
1068                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_OUTPUT_SUFFIX,
1069                                                         outfile_name
1070                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_SUFFIX,
1071                                                         outfile_name
1072                                                                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_OUTPUT_UNIQUE_SUFFIX,
1073                                                         outfile_name + "_indep_dc_gains_fitch_lca_ranks.txt",
1074                                                         outfile_name + "_indep_dc_gains_fitch_lca_taxonomies.txt",
1075                                                         outfile_name + "_indep_dc_gains_fitch_protein_statistics.txt",
1076                                                         protein_length_stats_by_dc,
1077                                                         domain_number_stats_by_dc,
1078                                                         domain_length_stats_by_domain );
1079         }
1080     }
1081
1082     public static void executeParsimonyAnalysisForSecondaryFeatures( final String outfile_name,
1083                                                                      final DomainParsimonyCalculator secondary_features_parsimony,
1084                                                                      final Phylogeny phylogeny,
1085                                                                      final String parameters_str,
1086                                                                      final Map<Species, MappingResults> mapping_results_map ) {
1087         final String sep = ForesterUtil.LINE_SEPARATOR + "###################" + ForesterUtil.LINE_SEPARATOR;
1088         final String date_time = ForesterUtil.getCurrentDateTime();
1089         System.out.println();
1090         writeToNexus( outfile_name + surfacing.NEXUS_SECONDARY_FEATURES,
1091                       secondary_features_parsimony.createMatrixOfSecondaryFeaturePresenceOrAbsence( null ),
1092                       phylogeny );
1093         Phylogeny local_phylogeny_copy = phylogeny.copy();
1094         secondary_features_parsimony.executeDolloParsimonyOnSecondaryFeatures( mapping_results_map );
1095         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossMatrix(), outfile_name
1096                 + surfacing.PARSIMONY_OUTPUT_GL_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
1097         SurfacingUtil.writeMatrixToFile( secondary_features_parsimony.getGainLossCountsMatrix(), outfile_name
1098                 + surfacing.PARSIMONY_OUTPUT_GL_COUNTS_SUFFIX_DOLLO_SECONDARY_FEATURES, Format.FORESTER );
1099         SurfacingUtil
1100                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1101                                                       CharacterStateMatrix.GainLossStates.GAIN,
1102                                                       outfile_name
1103                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_GAINS_SECONDARY_FEATURES,
1104                                                       sep,
1105                                                       ForesterUtil.LINE_SEPARATOR,
1106                                                       null );
1107         SurfacingUtil
1108                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1109                                                       CharacterStateMatrix.GainLossStates.LOSS,
1110                                                       outfile_name
1111                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_LOSSES_SECONDARY_FEATURES,
1112                                                       sep,
1113                                                       ForesterUtil.LINE_SEPARATOR,
1114                                                       null );
1115         SurfacingUtil
1116                 .writeBinaryStatesMatrixAsListToFile( secondary_features_parsimony.getGainLossMatrix(),
1117                                                       null,
1118                                                       outfile_name
1119                                                               + surfacing.PARSIMONY_OUTPUT_DOLLO_PRESENT_SECONDARY_FEATURES,
1120                                                       sep,
1121                                                       ForesterUtil.LINE_SEPARATOR,
1122                                                       null );
1123         preparePhylogeny( local_phylogeny_copy,
1124                           secondary_features_parsimony,
1125                           date_time,
1126                           "Dollo parsimony on secondary feature presence/absence",
1127                           "dollo_on_secondary_features_" + outfile_name,
1128                           parameters_str );
1129         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
1130                 + surfacing.SECONDARY_FEATURES_PARSIMONY_TREE_OUTPUT_SUFFIX_DOLLO );
1131         // FITCH DOMAIN COMBINATIONS
1132         // -------------------------
1133         local_phylogeny_copy = phylogeny.copy();
1134         final String randomization = "no";
1135         secondary_features_parsimony.executeFitchParsimonyOnBinaryDomainCombintionOnSecondaryFeatures( USE_LAST );
1136         preparePhylogeny( local_phylogeny_copy,
1137                           secondary_features_parsimony,
1138                           date_time,
1139                           "Fitch parsimony on secondary binary domain combination presence/absence randomization: "
1140                                   + randomization,
1141                           "fitch_on_binary_domain_combinations_" + outfile_name,
1142                           parameters_str );
1143         SurfacingUtil.writePhylogenyToFile( local_phylogeny_copy, outfile_name
1144                 + surfacing.BINARY_DOMAIN_COMBINATIONS_PARSIMONY_TREE_OUTPUT_SUFFIX_FITCH_MAPPED );
1145         calculateIndependentDomainCombinationGains( local_phylogeny_copy, outfile_name
1146                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_COUNTS_MAPPED_OUTPUT_SUFFIX, outfile_name
1147                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_MAPPED_OUTPUT_SUFFIX, outfile_name
1148                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_SUFFIX, outfile_name
1149                 + surfacing.INDEPENDENT_DC_GAINS_FITCH_PARS_DC_FOR_GO_MAPPING_MAPPED_OUTPUT_UNIQUE_SUFFIX, outfile_name
1150                 + "_MAPPED_indep_dc_gains_fitch_lca_ranks.txt", outfile_name
1151                 + "_MAPPED_indep_dc_gains_fitch_lca_taxonomies.txt", null, null, null, null );
1152     }
1153
1154     public static void doit( final List<Protein> proteins,
1155                              final List<DomainId> query_domain_ids_nc_order,
1156                              final Writer out,
1157                              final String separator,
1158                              final String limit_to_species,
1159                              final Map<String, List<Integer>> average_protein_lengths_by_dc ) throws IOException {
1160         for( final Protein protein : proteins ) {
1161             if ( ForesterUtil.isEmpty( limit_to_species )
1162                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1163                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1164                     out.write( protein.getSpecies().getSpeciesId() );
1165                     out.write( separator );
1166                     out.write( protein.getProteinId().getId() );
1167                     out.write( separator );
1168                     out.write( "[" );
1169                     final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
1170                     boolean first = true;
1171                     for( final Domain domain : protein.getProteinDomains() ) {
1172                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1173                             visited_domain_ids.add( domain.getDomainId() );
1174                             if ( first ) {
1175                                 first = false;
1176                             }
1177                             else {
1178                                 out.write( " " );
1179                             }
1180                             out.write( domain.getDomainId().getId() );
1181                             out.write( " {" );
1182                             out.write( "" + domain.getTotalCount() );
1183                             out.write( "}" );
1184                         }
1185                     }
1186                     out.write( "]" );
1187                     out.write( separator );
1188                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1189                             .equals( SurfacingConstants.NONE ) ) ) {
1190                         out.write( protein.getDescription() );
1191                     }
1192                     out.write( separator );
1193                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1194                             .equals( SurfacingConstants.NONE ) ) ) {
1195                         out.write( protein.getAccession() );
1196                     }
1197                     out.write( SurfacingConstants.NL );
1198                 }
1199             }
1200         }
1201         out.flush();
1202     }
1203
1204     public static void extractProteinNames( final List<Protein> proteins,
1205                                             final List<DomainId> query_domain_ids_nc_order,
1206                                             final Writer out,
1207                                             final String separator,
1208                                             final String limit_to_species ) throws IOException {
1209         for( final Protein protein : proteins ) {
1210             if ( ForesterUtil.isEmpty( limit_to_species )
1211                     || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1212                 if ( protein.contains( query_domain_ids_nc_order, true ) ) {
1213                     out.write( protein.getSpecies().getSpeciesId() );
1214                     out.write( separator );
1215                     out.write( protein.getProteinId().getId() );
1216                     out.write( separator );
1217                     out.write( "[" );
1218                     final Set<DomainId> visited_domain_ids = new HashSet<DomainId>();
1219                     boolean first = true;
1220                     for( final Domain domain : protein.getProteinDomains() ) {
1221                         if ( !visited_domain_ids.contains( domain.getDomainId() ) ) {
1222                             visited_domain_ids.add( domain.getDomainId() );
1223                             if ( first ) {
1224                                 first = false;
1225                             }
1226                             else {
1227                                 out.write( " " );
1228                             }
1229                             out.write( domain.getDomainId().getId() );
1230                             out.write( " {" );
1231                             out.write( "" + domain.getTotalCount() );
1232                             out.write( "}" );
1233                         }
1234                     }
1235                     out.write( "]" );
1236                     out.write( separator );
1237                     if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1238                             .equals( SurfacingConstants.NONE ) ) ) {
1239                         out.write( protein.getDescription() );
1240                     }
1241                     out.write( separator );
1242                     if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1243                             .equals( SurfacingConstants.NONE ) ) ) {
1244                         out.write( protein.getAccession() );
1245                     }
1246                     out.write( SurfacingConstants.NL );
1247                 }
1248             }
1249         }
1250         out.flush();
1251     }
1252
1253     public static void extractProteinNames( final SortedMap<Species, List<Protein>> protein_lists_per_species,
1254                                             final DomainId domain_id,
1255                                             final Writer out,
1256                                             final String separator,
1257                                             final String limit_to_species,
1258                                             final double domain_e_cutoff ) throws IOException {
1259         System.out.println( "Per domain E-value: " + domain_e_cutoff );
1260         for( final Species species : protein_lists_per_species.keySet() ) {
1261             System.out.println( species + ":" );
1262             for( final Protein protein : protein_lists_per_species.get( species ) ) {
1263                 if ( ForesterUtil.isEmpty( limit_to_species )
1264                         || protein.getSpecies().getSpeciesId().equalsIgnoreCase( limit_to_species ) ) {
1265                     final List<Domain> domains = protein.getProteinDomains( domain_id );
1266                     if ( domains.size() > 0 ) {
1267                         out.write( protein.getSpecies().getSpeciesId() );
1268                         out.write( separator );
1269                         out.write( protein.getProteinId().getId() );
1270                         out.write( separator );
1271                         out.write( domain_id.toString() );
1272                         out.write( separator );
1273                         int prev_to = -1;
1274                         for( final Domain domain : domains ) {
1275                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
1276                                 out.write( "/" );
1277                                 out.write( domain.getFrom() + "-" + domain.getTo() );
1278                                 if ( prev_to >= 0 ) {
1279                                     final int l = domain.getFrom() - prev_to;
1280                                     System.out.println( l );
1281                                 }
1282                                 prev_to = domain.getTo();
1283                             }
1284                         }
1285                         out.write( "/" );
1286                         out.write( separator );
1287                         final List<Domain> domain_list = new ArrayList<Domain>();
1288                         for( final Domain domain : protein.getProteinDomains() ) {
1289                             if ( ( domain_e_cutoff < 0 ) || ( domain.getPerDomainEvalue() <= domain_e_cutoff ) ) {
1290                                 domain_list.add( domain );
1291                             }
1292                         }
1293                         final Domain domain_ary[] = new Domain[ domain_list.size() ];
1294                         for( int i = 0; i < domain_list.size(); ++i ) {
1295                             domain_ary[ i ] = domain_list.get( i );
1296                         }
1297                         Arrays.sort( domain_ary, new DomainComparator( true ) );
1298                         out.write( "{" );
1299                         boolean first = true;
1300                         for( final Domain domain : domain_ary ) {
1301                             if ( first ) {
1302                                 first = false;
1303                             }
1304                             else {
1305                                 out.write( "," );
1306                             }
1307                             out.write( domain.getDomainId().toString() );
1308                             out.write( ":" + domain.getFrom() + "-" + domain.getTo() );
1309                             out.write( ":" + domain.getPerDomainEvalue() );
1310                         }
1311                         out.write( "}" );
1312                         if ( !( ForesterUtil.isEmpty( protein.getDescription() ) || protein.getDescription()
1313                                 .equals( SurfacingConstants.NONE ) ) ) {
1314                             out.write( protein.getDescription() );
1315                         }
1316                         out.write( separator );
1317                         if ( !( ForesterUtil.isEmpty( protein.getAccession() ) || protein.getAccession()
1318                                 .equals( SurfacingConstants.NONE ) ) ) {
1319                             out.write( protein.getAccession() );
1320                         }
1321                         out.write( SurfacingConstants.NL );
1322                     }
1323                 }
1324             }
1325         }
1326         out.flush();
1327     }
1328
1329     public static SortedSet<DomainId> getAllDomainIds( final List<GenomeWideCombinableDomains> gwcd_list ) {
1330         final SortedSet<DomainId> all_domains_ids = new TreeSet<DomainId>();
1331         for( final GenomeWideCombinableDomains gwcd : gwcd_list ) {
1332             final Set<DomainId> all_domains = gwcd.getAllDomainIds();
1333             //    for( final Domain domain : all_domains ) {
1334             all_domains_ids.addAll( all_domains );
1335             //    }
1336         }
1337         return all_domains_ids;
1338     }
1339
1340     public static SortedMap<String, Integer> getDomainCounts( final List<Protein> protein_domain_collections ) {
1341         final SortedMap<String, Integer> map = new TreeMap<String, Integer>();
1342         for( final Protein protein_domain_collection : protein_domain_collections ) {
1343             for( final Object name : protein_domain_collection.getProteinDomains() ) {
1344                 final BasicDomain protein_domain = ( BasicDomain ) name;
1345                 final String id = protein_domain.getDomainId().getId();
1346                 if ( map.containsKey( id ) ) {
1347                     map.put( id, map.get( id ) + 1 );
1348                 }
1349                 else {
1350                     map.put( id, 1 );
1351                 }
1352             }
1353         }
1354         return map;
1355     }
1356
1357     public static int getNumberOfNodesLackingName( final Phylogeny p, final StringBuilder names ) {
1358         final PhylogenyNodeIterator it = p.iteratorPostorder();
1359         int c = 0;
1360         while ( it.hasNext() ) {
1361             final PhylogenyNode n = it.next();
1362             if ( ForesterUtil.isEmpty( n.getName() )
1363                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1364                             .getScientificName() ) )
1365                     && ( !n.getNodeData().isHasTaxonomy() || ForesterUtil.isEmpty( n.getNodeData().getTaxonomy()
1366                             .getCommonName() ) ) ) {
1367                 if ( n.getParent() != null ) {
1368                     names.append( " " );
1369                     names.append( n.getParent().getName() );
1370                 }
1371                 final List l = n.getAllExternalDescendants();
1372                 for( final Object object : l ) {
1373                     System.out.println( l.toString() );
1374                 }
1375                 ++c;
1376             }
1377         }
1378         return c;
1379     }
1380
1381     /**
1382      * Returns true is Domain domain falls in an uninterrupted stretch of
1383      * covered positions.
1384      *
1385      * @param domain
1386      * @param covered_positions
1387      * @return
1388      */
1389     public static boolean isEngulfed( final Domain domain, final List<Boolean> covered_positions ) {
1390         for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1391             if ( ( i >= covered_positions.size() ) || ( covered_positions.get( i ) != true ) ) {
1392                 return false;
1393             }
1394         }
1395         return true;
1396     }
1397
1398     public static void preparePhylogeny( final Phylogeny p,
1399                                          final DomainParsimonyCalculator domain_parsimony,
1400                                          final String date_time,
1401                                          final String method,
1402                                          final String name,
1403                                          final String parameters_str ) {
1404         domain_parsimony.decoratePhylogenyWithDomains( p );
1405         final StringBuilder desc = new StringBuilder();
1406         desc.append( "[Method: " + method + "] [Date: " + date_time + "] " );
1407         desc.append( "[Cost: " + domain_parsimony.getCost() + "] " );
1408         desc.append( "[Gains: " + domain_parsimony.getTotalGains() + "] " );
1409         desc.append( "[Losses: " + domain_parsimony.getTotalLosses() + "] " );
1410         desc.append( "[Unchanged: " + domain_parsimony.getTotalUnchanged() + "] " );
1411         desc.append( "[Parameters: " + parameters_str + "]" );
1412         p.setName( name );
1413         p.setDescription( desc.toString() );
1414         p.setConfidence( new Confidence( domain_parsimony.getCost(), "parsimony" ) );
1415         p.setRerootable( false );
1416         p.setRooted( true );
1417     }
1418
1419     /*
1420      * species | protein id | n-terminal domain | c-terminal domain | n-terminal domain per domain E-value | c-terminal domain per domain E-value
1421      *
1422      *
1423      */
1424     static public StringBuffer proteinToDomainCombinations( final Protein protein,
1425                                                             final String protein_id,
1426                                                             final String separator ) {
1427         final StringBuffer sb = new StringBuffer();
1428         if ( protein.getSpecies() == null ) {
1429             throw new IllegalArgumentException( "species must not be null" );
1430         }
1431         if ( ForesterUtil.isEmpty( protein.getSpecies().getSpeciesId() ) ) {
1432             throw new IllegalArgumentException( "species id must not be empty" );
1433         }
1434         final List<Domain> domains = protein.getProteinDomains();
1435         if ( domains.size() > 1 ) {
1436             final Map<String, Integer> counts = new HashMap<String, Integer>();
1437             for( final Domain domain : domains ) {
1438                 final String id = domain.getDomainId().getId();
1439                 if ( counts.containsKey( id ) ) {
1440                     counts.put( id, counts.get( id ) + 1 );
1441                 }
1442                 else {
1443                     counts.put( id, 1 );
1444                 }
1445             }
1446             final Set<String> dcs = new HashSet<String>();
1447             for( int i = 1; i < domains.size(); ++i ) {
1448                 for( int j = 0; j < i; ++j ) {
1449                     Domain domain_n = domains.get( i );
1450                     Domain domain_c = domains.get( j );
1451                     if ( domain_n.getFrom() > domain_c.getFrom() ) {
1452                         domain_n = domains.get( j );
1453                         domain_c = domains.get( i );
1454                     }
1455                     final String dc = domain_n.getDomainId().getId() + domain_c.getDomainId().getId();
1456                     if ( !dcs.contains( dc ) ) {
1457                         dcs.add( dc );
1458                         sb.append( protein.getSpecies() );
1459                         sb.append( separator );
1460                         sb.append( protein_id );
1461                         sb.append( separator );
1462                         sb.append( domain_n.getDomainId().getId() );
1463                         sb.append( separator );
1464                         sb.append( domain_c.getDomainId().getId() );
1465                         sb.append( separator );
1466                         sb.append( domain_n.getPerDomainEvalue() );
1467                         sb.append( separator );
1468                         sb.append( domain_c.getPerDomainEvalue() );
1469                         sb.append( separator );
1470                         sb.append( counts.get( domain_n.getDomainId().getId() ) );
1471                         sb.append( separator );
1472                         sb.append( counts.get( domain_c.getDomainId().getId() ) );
1473                         sb.append( ForesterUtil.LINE_SEPARATOR );
1474                     }
1475                 }
1476             }
1477         }
1478         else if ( domains.size() == 1 ) {
1479             sb.append( protein.getSpecies() );
1480             sb.append( separator );
1481             sb.append( protein_id );
1482             sb.append( separator );
1483             sb.append( domains.get( 0 ).getDomainId().getId() );
1484             sb.append( separator );
1485             sb.append( separator );
1486             sb.append( domains.get( 0 ).getPerDomainEvalue() );
1487             sb.append( separator );
1488             sb.append( separator );
1489             sb.append( 1 );
1490             sb.append( separator );
1491             sb.append( ForesterUtil.LINE_SEPARATOR );
1492         }
1493         else {
1494             sb.append( protein.getSpecies() );
1495             sb.append( separator );
1496             sb.append( protein_id );
1497             sb.append( separator );
1498             sb.append( separator );
1499             sb.append( separator );
1500             sb.append( separator );
1501             sb.append( separator );
1502             sb.append( separator );
1503             sb.append( ForesterUtil.LINE_SEPARATOR );
1504         }
1505         return sb;
1506     }
1507
1508     /**
1509      *
1510      * Example regarding engulfment: ------------0.1 ----------0.2 --0.3 =>
1511      * domain with 0.3 is ignored
1512      *
1513      * -----------0.1 ----------0.2 --0.3 => domain with 0.3 is ignored
1514      *
1515      *
1516      * ------------0.1 ----------0.3 --0.2 => domains with 0.3 and 0.2 are _not_
1517      * ignored
1518      *
1519      * @param max_allowed_overlap
1520      *            maximal allowed overlap (inclusive) to be still considered not
1521      *            overlapping (zero or negative value to allow any overlap)
1522      * @param remove_engulfed_domains
1523      *            to remove domains which are completely engulfed by coverage of
1524      *            domains with better support
1525      * @param protein
1526      * @return
1527      */
1528     public static Protein removeOverlappingDomains( final int max_allowed_overlap,
1529                                                     final boolean remove_engulfed_domains,
1530                                                     final Protein protein ) {
1531         final Protein pruned_protein = new BasicProtein( protein.getProteinId().getId(), protein.getSpecies()
1532                 .getSpeciesId(), protein.getLength() );
1533         final List<Domain> sorted = SurfacingUtil.sortDomainsWithAscendingConfidenceValues( protein );
1534         final List<Boolean> covered_positions = new ArrayList<Boolean>();
1535         for( final Domain domain : sorted ) {
1536             if ( ( ( max_allowed_overlap < 0 ) || ( SurfacingUtil.calculateOverlap( domain, covered_positions ) <= max_allowed_overlap ) )
1537                     && ( !remove_engulfed_domains || !isEngulfed( domain, covered_positions ) ) ) {
1538                 final int covered_positions_size = covered_positions.size();
1539                 for( int i = covered_positions_size; i < domain.getFrom(); ++i ) {
1540                     covered_positions.add( false );
1541                 }
1542                 final int new_covered_positions_size = covered_positions.size();
1543                 for( int i = domain.getFrom(); i <= domain.getTo(); ++i ) {
1544                     if ( i < new_covered_positions_size ) {
1545                         covered_positions.set( i, true );
1546                     }
1547                     else {
1548                         covered_positions.add( true );
1549                     }
1550                 }
1551                 pruned_protein.addProteinDomain( domain );
1552             }
1553         }
1554         return pruned_protein;
1555     }
1556
1557     public static List<Domain> sortDomainsWithAscendingConfidenceValues( final Protein protein ) {
1558         final List<Domain> domains = new ArrayList<Domain>();
1559         for( final Domain d : protein.getProteinDomains() ) {
1560             domains.add( d );
1561         }
1562         Collections.sort( domains, SurfacingUtil.ASCENDING_CONFIDENCE_VALUE_ORDER );
1563         return domains;
1564     }
1565
1566     private static List<String> splitDomainCombination( final String dc ) {
1567         final String[] s = dc.split( "=" );
1568         if ( s.length != 2 ) {
1569             ForesterUtil.printErrorMessage( surfacing.PRG_NAME, "Stringyfied domain combination has illegal format: "
1570                     + dc );
1571             System.exit( -1 );
1572         }
1573         final List<String> l = new ArrayList<String>( 2 );
1574         l.add( s[ 0 ] );
1575         l.add( s[ 1 ] );
1576         return l;
1577     }
1578
1579     public static void writeAllDomainsChangedOnAllSubtrees( final Phylogeny p,
1580                                                             final boolean get_gains,
1581                                                             final String outdir,
1582                                                             final String suffix_for_filename ) throws IOException {
1583         CharacterStateMatrix.GainLossStates state = CharacterStateMatrix.GainLossStates.GAIN;
1584         if ( !get_gains ) {
1585             state = CharacterStateMatrix.GainLossStates.LOSS;
1586         }
1587         final File base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_SUBTREE_DOMAIN_GAIN_LOSS_FILES,
1588                                                                   false,
1589                                                                   state,
1590                                                                   outdir );
1591         for( final PhylogenyNodeIterator it = p.iteratorPostorder(); it.hasNext(); ) {
1592             final PhylogenyNode node = it.next();
1593             if ( !node.isExternal() ) {
1594                 final SortedSet<String> domains = collectAllDomainsChangedOnSubtree( node, get_gains );
1595                 if ( domains.size() > 0 ) {
1596                     final Writer writer = ForesterUtil.createBufferedWriter( base_dir + ForesterUtil.FILE_SEPARATOR
1597                             + node.getName() + suffix_for_filename );
1598                     for( final String domain : domains ) {
1599                         writer.write( domain );
1600                         writer.write( ForesterUtil.LINE_SEPARATOR );
1601                     }
1602                     writer.close();
1603                 }
1604             }
1605         }
1606     }
1607
1608     private static void writeAllEncounteredPfamsToFile( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1609                                                         final Map<GoId, GoTerm> go_id_to_term_map,
1610                                                         final String outfile_name,
1611                                                         final SortedSet<String> all_pfams_encountered ) {
1612         final File all_pfams_encountered_file = new File( outfile_name + surfacing.ALL_PFAMS_ENCOUNTERED_SUFFIX );
1613         final File all_pfams_encountered_with_go_annotation_file = new File( outfile_name
1614                 + surfacing.ALL_PFAMS_ENCOUNTERED_WITH_GO_ANNOTATION_SUFFIX );
1615         final File encountered_pfams_summary_file = new File( outfile_name + surfacing.ENCOUNTERED_PFAMS_SUMMARY_SUFFIX );
1616         int biological_process_counter = 0;
1617         int cellular_component_counter = 0;
1618         int molecular_function_counter = 0;
1619         int pfams_with_mappings_counter = 0;
1620         int pfams_without_mappings_counter = 0;
1621         int pfams_without_mappings_to_bp_or_mf_counter = 0;
1622         int pfams_with_mappings_to_bp_or_mf_counter = 0;
1623         try {
1624             final Writer all_pfams_encountered_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_file ) );
1625             final Writer all_pfams_encountered_with_go_annotation_writer = new BufferedWriter( new FileWriter( all_pfams_encountered_with_go_annotation_file ) );
1626             final Writer summary_writer = new BufferedWriter( new FileWriter( encountered_pfams_summary_file ) );
1627             summary_writer.write( "# Pfam to GO mapping summary" );
1628             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1629             summary_writer.write( "# Actual summary is at the end of this file." );
1630             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1631             summary_writer.write( "# Encountered Pfams without a GO mapping:" );
1632             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1633             for( final String pfam : all_pfams_encountered ) {
1634                 all_pfams_encountered_writer.write( pfam );
1635                 all_pfams_encountered_writer.write( ForesterUtil.LINE_SEPARATOR );
1636                 final DomainId domain_id = new DomainId( pfam );
1637                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
1638                     ++pfams_with_mappings_counter;
1639                     all_pfams_encountered_with_go_annotation_writer.write( pfam );
1640                     all_pfams_encountered_with_go_annotation_writer.write( ForesterUtil.LINE_SEPARATOR );
1641                     final List<GoId> go_ids = domain_id_to_go_ids_map.get( domain_id );
1642                     boolean maps_to_bp = false;
1643                     boolean maps_to_cc = false;
1644                     boolean maps_to_mf = false;
1645                     for( final GoId go_id : go_ids ) {
1646                         final GoTerm go_term = go_id_to_term_map.get( go_id );
1647                         if ( go_term.getGoNameSpace().isBiologicalProcess() ) {
1648                             maps_to_bp = true;
1649                         }
1650                         else if ( go_term.getGoNameSpace().isCellularComponent() ) {
1651                             maps_to_cc = true;
1652                         }
1653                         else if ( go_term.getGoNameSpace().isMolecularFunction() ) {
1654                             maps_to_mf = true;
1655                         }
1656                     }
1657                     if ( maps_to_bp ) {
1658                         ++biological_process_counter;
1659                     }
1660                     if ( maps_to_cc ) {
1661                         ++cellular_component_counter;
1662                     }
1663                     if ( maps_to_mf ) {
1664                         ++molecular_function_counter;
1665                     }
1666                     if ( maps_to_bp || maps_to_mf ) {
1667                         ++pfams_with_mappings_to_bp_or_mf_counter;
1668                     }
1669                     else {
1670                         ++pfams_without_mappings_to_bp_or_mf_counter;
1671                     }
1672                 }
1673                 else {
1674                     ++pfams_without_mappings_to_bp_or_mf_counter;
1675                     ++pfams_without_mappings_counter;
1676                     summary_writer.write( pfam );
1677                     summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1678                 }
1679             }
1680             all_pfams_encountered_writer.close();
1681             all_pfams_encountered_with_go_annotation_writer.close();
1682             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + all_pfams_encountered.size()
1683                     + "] encountered Pfams to: \"" + all_pfams_encountered_file + "\"" );
1684             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote all [" + pfams_with_mappings_counter
1685                     + "] encountered Pfams with GO mappings to: \"" + all_pfams_encountered_with_go_annotation_file
1686                     + "\"" );
1687             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote summary (including all ["
1688                     + pfams_without_mappings_counter + "] encountered Pfams without GO mappings) to: \""
1689                     + encountered_pfams_summary_file + "\"" );
1690             ForesterUtil.programMessage( surfacing.PRG_NAME, "Sum of Pfams encountered                : "
1691                     + all_pfams_encountered.size() );
1692             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without a mapping                 : "
1693                     + pfams_without_mappings_counter + " ["
1694                     + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
1695             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams without mapping to proc. or func. : "
1696                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1697                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
1698             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping                    : "
1699                     + pfams_with_mappings_counter + " ["
1700                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
1701             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with a mapping to proc. or func.  : "
1702                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1703                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
1704             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to biological process: "
1705                     + biological_process_counter + " ["
1706                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
1707             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to molecular function: "
1708                     + molecular_function_counter + " ["
1709                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
1710             ForesterUtil.programMessage( surfacing.PRG_NAME, "Pfams with mapping to cellular component: "
1711                     + cellular_component_counter + " ["
1712                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
1713             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1714             summary_writer.write( "# Sum of Pfams encountered                : " + all_pfams_encountered.size() );
1715             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1716             summary_writer.write( "# Pfams without a mapping                 : " + pfams_without_mappings_counter
1717                     + " [" + ( ( 100 * pfams_without_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
1718             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1719             summary_writer.write( "# Pfams without mapping to proc. or func. : "
1720                     + pfams_without_mappings_to_bp_or_mf_counter + " ["
1721                     + ( ( 100 * pfams_without_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
1722             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1723             summary_writer.write( "# Pfams with a mapping                    : " + pfams_with_mappings_counter + " ["
1724                     + ( ( 100 * pfams_with_mappings_counter ) / all_pfams_encountered.size() ) + "%]" );
1725             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1726             summary_writer.write( "# Pfams with a mapping to proc. or func.  : "
1727                     + pfams_with_mappings_to_bp_or_mf_counter + " ["
1728                     + ( ( 100 * pfams_with_mappings_to_bp_or_mf_counter ) / all_pfams_encountered.size() ) + "%]" );
1729             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1730             summary_writer.write( "# Pfams with mapping to biological process: " + biological_process_counter + " ["
1731                     + ( ( 100 * biological_process_counter ) / all_pfams_encountered.size() ) + "%]" );
1732             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1733             summary_writer.write( "# Pfams with mapping to molecular function: " + molecular_function_counter + " ["
1734                     + ( ( 100 * molecular_function_counter ) / all_pfams_encountered.size() ) + "%]" );
1735             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1736             summary_writer.write( "# Pfams with mapping to cellular component: " + cellular_component_counter + " ["
1737                     + ( ( 100 * cellular_component_counter ) / all_pfams_encountered.size() ) + "%]" );
1738             summary_writer.write( ForesterUtil.LINE_SEPARATOR );
1739             summary_writer.close();
1740         }
1741         catch ( final IOException e ) {
1742             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
1743         }
1744     }
1745
1746     public static void writeBinaryDomainCombinationsFileForGraphAnalysis( final String[][] input_file_properties,
1747                                                                           final File output_dir,
1748                                                                           final GenomeWideCombinableDomains gwcd,
1749                                                                           final int i,
1750                                                                           final GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
1751         File dc_outfile_dot = new File( input_file_properties[ i ][ 0 ]
1752                 + surfacing.DOMAIN_COMBINITONS_OUTPUTFILE_SUFFIX_FOR_GRAPH_ANALYSIS );
1753         if ( output_dir != null ) {
1754             dc_outfile_dot = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile_dot );
1755         }
1756         checkForOutputFileWriteability( dc_outfile_dot );
1757         final SortedSet<BinaryDomainCombination> binary_combinations = createSetOfAllBinaryDomainCombinationsPerGenome( gwcd );
1758         try {
1759             final BufferedWriter out_dot = new BufferedWriter( new FileWriter( dc_outfile_dot ) );
1760             for( final BinaryDomainCombination bdc : binary_combinations ) {
1761                 out_dot.write( bdc.toGraphDescribingLanguage( BinaryDomainCombination.OutputFormat.DOT, null, null )
1762                         .toString() );
1763                 out_dot.write( SurfacingConstants.NL );
1764             }
1765             out_dot.close();
1766         }
1767         catch ( final IOException e ) {
1768             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1769         }
1770         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote binary domain combination for \""
1771                 + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
1772                 + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile_dot + "\"" );
1773     }
1774
1775     public static void writeBinaryStatesMatrixAsListToFile( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1776                                                             final CharacterStateMatrix.GainLossStates state,
1777                                                             final String filename,
1778                                                             final String indentifier_characters_separator,
1779                                                             final String character_separator,
1780                                                             final Map<String, String> descriptions ) {
1781         final File outfile = new File( filename );
1782         checkForOutputFileWriteability( outfile );
1783         final SortedSet<String> sorted_ids = new TreeSet<String>();
1784         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1785             sorted_ids.add( matrix.getIdentifier( i ) );
1786         }
1787         try {
1788             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1789             for( final String id : sorted_ids ) {
1790                 out.write( indentifier_characters_separator );
1791                 out.write( "#" + id );
1792                 out.write( indentifier_characters_separator );
1793                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1794                     // Not nice:
1795                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1796                     if ( ( matrix.getState( id, c ) == state )
1797                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1798                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1799                         out.write( matrix.getCharacter( c ) );
1800                         if ( ( descriptions != null ) && !descriptions.isEmpty()
1801                                 && descriptions.containsKey( matrix.getCharacter( c ) ) ) {
1802                             out.write( "\t" );
1803                             out.write( descriptions.get( matrix.getCharacter( c ) ) );
1804                         }
1805                         out.write( character_separator );
1806                     }
1807                 }
1808             }
1809             out.flush();
1810             out.close();
1811         }
1812         catch ( final IOException e ) {
1813             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1814         }
1815         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1816     }
1817
1818     public static void writeBinaryStatesMatrixAsListToFileForBinaryCombinationsForGraphAnalysis( final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1819                                                                                                  final CharacterStateMatrix.GainLossStates state,
1820                                                                                                  final String filename,
1821                                                                                                  final String indentifier_characters_separator,
1822                                                                                                  final String character_separator,
1823                                                                                                  final BinaryDomainCombination.OutputFormat bc_output_format ) {
1824         final File outfile = new File( filename );
1825         checkForOutputFileWriteability( outfile );
1826         final SortedSet<String> sorted_ids = new TreeSet<String>();
1827         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1828             sorted_ids.add( matrix.getIdentifier( i ) );
1829         }
1830         try {
1831             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
1832             for( final String id : sorted_ids ) {
1833                 out.write( indentifier_characters_separator );
1834                 out.write( "#" + id );
1835                 out.write( indentifier_characters_separator );
1836                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1837                     // Not nice:
1838                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1839                     if ( ( matrix.getState( id, c ) == state )
1840                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) || ( matrix
1841                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) ) ) ) {
1842                         BinaryDomainCombination bdc = null;
1843                         try {
1844                             bdc = BasicBinaryDomainCombination.createInstance( matrix.getCharacter( c ) );
1845                         }
1846                         catch ( final Exception e ) {
1847                             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getLocalizedMessage() );
1848                         }
1849                         out.write( bdc.toGraphDescribingLanguage( bc_output_format, null, null ).toString() );
1850                         out.write( character_separator );
1851                     }
1852                 }
1853             }
1854             out.flush();
1855             out.close();
1856         }
1857         catch ( final IOException e ) {
1858             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
1859         }
1860         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters list: \"" + filename + "\"" );
1861     }
1862
1863     public static void writeBinaryStatesMatrixToList( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
1864                                                       final Map<GoId, GoTerm> go_id_to_term_map,
1865                                                       final GoNameSpace go_namespace_limit,
1866                                                       final boolean domain_combinations,
1867                                                       final CharacterStateMatrix<CharacterStateMatrix.GainLossStates> matrix,
1868                                                       final CharacterStateMatrix.GainLossStates state,
1869                                                       final String filename,
1870                                                       final String indentifier_characters_separator,
1871                                                       final String character_separator,
1872                                                       final String title_for_html,
1873                                                       final String prefix_for_html,
1874                                                       final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
1875                                                       final SortedSet<String> all_pfams_encountered,
1876                                                       final SortedSet<String> pfams_gained_or_lost,
1877                                                       final String suffix_for_per_node_events_file ) {
1878         if ( ( go_namespace_limit != null ) && ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1879             throw new IllegalArgumentException( "attempt to use GO namespace limit without a GO-id to term map" );
1880         }
1881         else if ( ( ( domain_id_to_go_ids_map == null ) || ( domain_id_to_go_ids_map.size() < 1 ) ) ) {
1882             throw new IllegalArgumentException( "attempt to output detailed HTML without a Pfam to GO map" );
1883         }
1884         else if ( ( ( go_id_to_term_map == null ) || ( go_id_to_term_map.size() < 1 ) ) ) {
1885             throw new IllegalArgumentException( "attempt to output detailed HTML without a GO-id to term map" );
1886         }
1887         final File outfile = new File( filename );
1888         checkForOutputFileWriteability( outfile );
1889         final SortedSet<String> sorted_ids = new TreeSet<String>();
1890         for( int i = 0; i < matrix.getNumberOfIdentifiers(); ++i ) {
1891             sorted_ids.add( matrix.getIdentifier( i ) );
1892         }
1893         try {
1894             final Writer out = new BufferedWriter( new FileWriter( outfile ) );
1895             final File per_node_go_mapped_domain_gain_loss_files_base_dir = createBaseDirForPerNodeDomainFiles( surfacing.BASE_DIRECTORY_PER_NODE_DOMAIN_GAIN_LOSS_FILES,
1896                                                                                                                 domain_combinations,
1897                                                                                                                 state,
1898                                                                                                                 filename );
1899             Writer per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1900             File per_node_go_mapped_domain_gain_loss_outfile = null;
1901             int per_node_counter = 0;
1902             out.write( "<html>" );
1903             out.write( SurfacingConstants.NL );
1904             addHtmlHead( out, title_for_html );
1905             out.write( SurfacingConstants.NL );
1906             out.write( "<body>" );
1907             out.write( SurfacingConstants.NL );
1908             out.write( "<h1>" );
1909             out.write( SurfacingConstants.NL );
1910             out.write( title_for_html );
1911             out.write( SurfacingConstants.NL );
1912             out.write( "</h1>" );
1913             out.write( SurfacingConstants.NL );
1914             out.write( "<table>" );
1915             out.write( SurfacingConstants.NL );
1916             for( final String id : sorted_ids ) {
1917                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1918                 if ( matcher.matches() ) {
1919                     continue;
1920                 }
1921                 out.write( "<tr>" );
1922                 out.write( "<td>" );
1923                 out.write( "<a href=\"#" + id + "\">" + id + "</a>" );
1924                 out.write( "</td>" );
1925                 out.write( "</tr>" );
1926                 out.write( SurfacingConstants.NL );
1927             }
1928             out.write( "</table>" );
1929             out.write( SurfacingConstants.NL );
1930             for( final String id : sorted_ids ) {
1931                 final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( id );
1932                 if ( matcher.matches() ) {
1933                     continue;
1934                 }
1935                 out.write( SurfacingConstants.NL );
1936                 out.write( "<h2>" );
1937                 out.write( "<a name=\"" + id + "\">" + id + "</a>" );
1938                 writeTaxonomyLinks( out, id );
1939                 out.write( "</h2>" );
1940                 out.write( SurfacingConstants.NL );
1941                 out.write( "<table>" );
1942                 out.write( SurfacingConstants.NL );
1943                 out.write( "<tr>" );
1944                 out.write( "<td><b>" );
1945                 out.write( "Pfam domain(s)" );
1946                 out.write( "</b></td><td><b>" );
1947                 out.write( "GO term acc" );
1948                 out.write( "</b></td><td><b>" );
1949                 out.write( "GO term" );
1950                 out.write( "</b></td><td><b>" );
1951                 out.write( "GO namespace" );
1952                 out.write( "</b></td>" );
1953                 out.write( "</tr>" );
1954                 out.write( SurfacingConstants.NL );
1955                 out.write( "</tr>" );
1956                 out.write( SurfacingConstants.NL );
1957                 per_node_counter = 0;
1958                 if ( matrix.getNumberOfCharacters() > 0 ) {
1959                     per_node_go_mapped_domain_gain_loss_outfile = new File( per_node_go_mapped_domain_gain_loss_files_base_dir
1960                             + ForesterUtil.FILE_SEPARATOR + id + suffix_for_per_node_events_file );
1961                     SurfacingUtil.checkForOutputFileWriteability( per_node_go_mapped_domain_gain_loss_outfile );
1962                     per_node_go_mapped_domain_gain_loss_outfile_writer = ForesterUtil
1963                             .createBufferedWriter( per_node_go_mapped_domain_gain_loss_outfile );
1964                 }
1965                 else {
1966                     per_node_go_mapped_domain_gain_loss_outfile = null;
1967                     per_node_go_mapped_domain_gain_loss_outfile_writer = null;
1968                 }
1969                 for( int c = 0; c < matrix.getNumberOfCharacters(); ++c ) {
1970                     // Not nice:
1971                     // using null to indicate either UNCHANGED_PRESENT or GAIN.
1972                     if ( ( matrix.getState( id, c ) == state )
1973                             || ( ( state == null ) && ( ( matrix.getState( id, c ) == CharacterStateMatrix.GainLossStates.UNCHANGED_PRESENT ) || ( matrix
1974                                     .getState( id, c ) == CharacterStateMatrix.GainLossStates.GAIN ) ) ) ) {
1975                         final String character = matrix.getCharacter( c );
1976                         String domain_0 = "";
1977                         String domain_1 = "";
1978                         if ( character.indexOf( BinaryDomainCombination.SEPARATOR ) > 0 ) {
1979                             final String[] s = character.split( BinaryDomainCombination.SEPARATOR );
1980                             if ( s.length != 2 ) {
1981                                 throw new AssertionError( "this should not have happened: unexpected format for domain combination: ["
1982                                         + character + "]" );
1983                             }
1984                             domain_0 = s[ 0 ];
1985                             domain_1 = s[ 1 ];
1986                         }
1987                         else {
1988                             domain_0 = character;
1989                         }
1990                         writeDomainData( domain_id_to_go_ids_map,
1991                                          go_id_to_term_map,
1992                                          go_namespace_limit,
1993                                          out,
1994                                          domain_0,
1995                                          domain_1,
1996                                          prefix_for_html,
1997                                          character_separator,
1998                                          domain_id_to_secondary_features_maps,
1999                                          null );
2000                         all_pfams_encountered.add( domain_0 );
2001                         if ( pfams_gained_or_lost != null ) {
2002                             pfams_gained_or_lost.add( domain_0 );
2003                         }
2004                         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2005                             all_pfams_encountered.add( domain_1 );
2006                             if ( pfams_gained_or_lost != null ) {
2007                                 pfams_gained_or_lost.add( domain_1 );
2008                             }
2009                         }
2010                         if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
2011                             writeDomainsToIndividualFilePerTreeNode( per_node_go_mapped_domain_gain_loss_outfile_writer,
2012                                                                      domain_0,
2013                                                                      domain_1 );
2014                             per_node_counter++;
2015                         }
2016                     }
2017                 }
2018                 if ( per_node_go_mapped_domain_gain_loss_outfile_writer != null ) {
2019                     per_node_go_mapped_domain_gain_loss_outfile_writer.close();
2020                     if ( per_node_counter < 1 ) {
2021                         per_node_go_mapped_domain_gain_loss_outfile.delete();
2022                     }
2023                     per_node_counter = 0;
2024                 }
2025                 out.write( "</table>" );
2026                 out.write( SurfacingConstants.NL );
2027                 out.write( "<hr>" );
2028                 out.write( SurfacingConstants.NL );
2029             } // for( final String id : sorted_ids ) {
2030             out.write( "</body>" );
2031             out.write( SurfacingConstants.NL );
2032             out.write( "</html>" );
2033             out.write( SurfacingConstants.NL );
2034             out.flush();
2035             out.close();
2036         }
2037         catch ( final IOException e ) {
2038             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2039         }
2040         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote characters detailed HTML list: \"" + filename + "\"" );
2041     }
2042
2043     public static void writeDomainCombinationsCountsFile( final String[][] input_file_properties,
2044                                                           final File output_dir,
2045                                                           final Writer per_genome_domain_promiscuity_statistics_writer,
2046                                                           final GenomeWideCombinableDomains gwcd,
2047                                                           final int i,
2048                                                           final GenomeWideCombinableDomains.GenomeWideCombinableDomainsSortOrder dc_sort_order ) {
2049         File dc_outfile = new File( input_file_properties[ i ][ 0 ]
2050                 + surfacing.DOMAIN_COMBINITON_COUNTS_OUTPUTFILE_SUFFIX );
2051         if ( output_dir != null ) {
2052             dc_outfile = new File( output_dir + ForesterUtil.FILE_SEPARATOR + dc_outfile );
2053         }
2054         checkForOutputFileWriteability( dc_outfile );
2055         try {
2056             final BufferedWriter out = new BufferedWriter( new FileWriter( dc_outfile ) );
2057             out.write( gwcd.toStringBuilder( dc_sort_order ).toString() );
2058             out.close();
2059         }
2060         catch ( final IOException e ) {
2061             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2062         }
2063         final DescriptiveStatistics stats = gwcd.getPerGenomeDomainPromiscuityStatistics();
2064         try {
2065             per_genome_domain_promiscuity_statistics_writer.write( input_file_properties[ i ][ 0 ] + "\t" );
2066             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.arithmeticMean() ) + "\t" );
2067             if ( stats.getN() < 2 ) {
2068                 per_genome_domain_promiscuity_statistics_writer.write( "n/a" + "\t" );
2069             }
2070             else {
2071                 per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats
2072                         .sampleStandardDeviation() ) + "\t" );
2073             }
2074             per_genome_domain_promiscuity_statistics_writer.write( FORMATTER_3.format( stats.median() ) + "\t" );
2075             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMin() + "\t" );
2076             per_genome_domain_promiscuity_statistics_writer.write( ( int ) stats.getMax() + "\t" );
2077             per_genome_domain_promiscuity_statistics_writer.write( stats.getN() + "\t" );
2078             final SortedSet<DomainId> mpds = gwcd.getMostPromiscuosDomain();
2079             for( final DomainId mpd : mpds ) {
2080                 per_genome_domain_promiscuity_statistics_writer.write( mpd.getId() + " " );
2081             }
2082             per_genome_domain_promiscuity_statistics_writer.write( ForesterUtil.LINE_SEPARATOR );
2083         }
2084         catch ( final IOException e ) {
2085             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2086         }
2087         if ( input_file_properties[ i ].length == 3 ) {
2088             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2089                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ", "
2090                     + input_file_properties[ i ][ 2 ] + ") to: \"" + dc_outfile + "\"" );
2091         }
2092         else {
2093             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote domain combination counts for \""
2094                     + input_file_properties[ i ][ 0 ] + "\" (" + input_file_properties[ i ][ 1 ] + ") to: \""
2095                     + dc_outfile + "\"" );
2096         }
2097     }
2098
2099     private static void writeDomainData( final Map<DomainId, List<GoId>> domain_id_to_go_ids_map,
2100                                          final Map<GoId, GoTerm> go_id_to_term_map,
2101                                          final GoNameSpace go_namespace_limit,
2102                                          final Writer out,
2103                                          final String domain_0,
2104                                          final String domain_1,
2105                                          final String prefix_for_html,
2106                                          final String character_separator_for_non_html_output,
2107                                          final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps,
2108                                          final Set<GoId> all_go_ids ) throws IOException {
2109         boolean any_go_annotation_present = false;
2110         boolean first_has_no_go = false;
2111         int domain_count = 2; // To distinguish between domains and binary domain combinations.
2112         if ( ForesterUtil.isEmpty( domain_1 ) ) {
2113             domain_count = 1;
2114         }
2115         // The following has a difficult to understand logic.
2116         for( int d = 0; d < domain_count; ++d ) {
2117             List<GoId> go_ids = null;
2118             boolean go_annotation_present = false;
2119             if ( d == 0 ) {
2120                 final DomainId domain_id = new DomainId( domain_0 );
2121                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2122                     go_annotation_present = true;
2123                     any_go_annotation_present = true;
2124                     go_ids = domain_id_to_go_ids_map.get( domain_id );
2125                 }
2126                 else {
2127                     first_has_no_go = true;
2128                 }
2129             }
2130             else {
2131                 final DomainId domain_id = new DomainId( domain_1 );
2132                 if ( domain_id_to_go_ids_map.containsKey( domain_id ) ) {
2133                     go_annotation_present = true;
2134                     any_go_annotation_present = true;
2135                     go_ids = domain_id_to_go_ids_map.get( domain_id );
2136                 }
2137             }
2138             if ( go_annotation_present ) {
2139                 boolean first = ( ( d == 0 ) || ( ( d == 1 ) && first_has_no_go ) );
2140                 for( final GoId go_id : go_ids ) {
2141                     out.write( "<tr>" );
2142                     if ( first ) {
2143                         first = false;
2144                         writeDomainIdsToHtml( out,
2145                                               domain_0,
2146                                               domain_1,
2147                                               prefix_for_html,
2148                                               domain_id_to_secondary_features_maps );
2149                     }
2150                     else {
2151                         out.write( "<td></td>" );
2152                     }
2153                     if ( !go_id_to_term_map.containsKey( go_id ) ) {
2154                         throw new IllegalArgumentException( "GO-id [" + go_id + "] not found in GO-id to GO-term map" );
2155                     }
2156                     final GoTerm go_term = go_id_to_term_map.get( go_id );
2157                     if ( ( go_namespace_limit == null ) || go_namespace_limit.equals( go_term.getGoNameSpace() ) ) {
2158                         // final String top = GoUtils.getPenultimateGoTerm( go_term, go_id_to_term_map ).getName();
2159                         final String go_id_str = go_id.getId();
2160                         out.write( "<td>" );
2161                         out.write( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id_str
2162                                 + "\" target=\"amigo_window\">" + go_id_str + "</a>" );
2163                         out.write( "</td><td>" );
2164                         out.write( go_term.getName() );
2165                         if ( domain_count == 2 ) {
2166                             out.write( " (" + d + ")" );
2167                         }
2168                         out.write( "</td><td>" );
2169                         // out.write( top );
2170                         // out.write( "</td><td>" );
2171                         out.write( "[" );
2172                         out.write( go_term.getGoNameSpace().toShortString() );
2173                         out.write( "]" );
2174                         out.write( "</td>" );
2175                         if ( all_go_ids != null ) {
2176                             all_go_ids.add( go_id );
2177                         }
2178                     }
2179                     else {
2180                         out.write( "<td>" );
2181                         out.write( "</td><td>" );
2182                         out.write( "</td><td>" );
2183                         out.write( "</td><td>" );
2184                         out.write( "</td>" );
2185                     }
2186                     out.write( "</tr>" );
2187                     out.write( SurfacingConstants.NL );
2188                 }
2189             }
2190         } //  for( int d = 0; d < domain_count; ++d )
2191         if ( !any_go_annotation_present ) {
2192             out.write( "<tr>" );
2193             writeDomainIdsToHtml( out, domain_0, domain_1, prefix_for_html, domain_id_to_secondary_features_maps );
2194             out.write( "<td>" );
2195             out.write( "</td><td>" );
2196             out.write( "</td><td>" );
2197             out.write( "</td><td>" );
2198             out.write( "</td>" );
2199             out.write( "</tr>" );
2200             out.write( SurfacingConstants.NL );
2201         }
2202     }
2203
2204     private static void writeDomainIdsToHtml( final Writer out,
2205                                               final String domain_0,
2206                                               final String domain_1,
2207                                               final String prefix_for_detailed_html,
2208                                               final Map<DomainId, Set<String>>[] domain_id_to_secondary_features_maps )
2209             throws IOException {
2210         out.write( "<td>" );
2211         if ( !ForesterUtil.isEmpty( prefix_for_detailed_html ) ) {
2212             out.write( prefix_for_detailed_html );
2213             out.write( " " );
2214         }
2215         out.write( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + domain_0 + "\">" + domain_0 + "</a>" );
2216         out.write( "</td>" );
2217     }
2218
2219     public static DescriptiveStatistics writeDomainSimilaritiesToFile( final StringBuilder html_desc,
2220                                                                        final StringBuilder html_title,
2221                                                                        final Writer single_writer,
2222                                                                        Map<Character, Writer> split_writers,
2223                                                                        final SortedSet<DomainSimilarity> similarities,
2224                                                                        final boolean treat_as_binary,
2225                                                                        final List<Species> species_order,
2226                                                                        final PrintableDomainSimilarity.PRINT_OPTION print_option,
2227                                                                        final DomainSimilarity.DomainSimilaritySortField sort_field,
2228                                                                        final DomainSimilarity.DomainSimilarityScoring scoring,
2229                                                                        final boolean verbose ) throws IOException {
2230         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2231         String histogram_title = null;
2232         switch ( sort_field ) {
2233             case ABS_MAX_COUNTS_DIFFERENCE:
2234                 if ( treat_as_binary ) {
2235                     histogram_title = "absolute counts difference:";
2236                 }
2237                 else {
2238                     histogram_title = "absolute (maximal) counts difference:";
2239                 }
2240                 break;
2241             case MAX_COUNTS_DIFFERENCE:
2242                 if ( treat_as_binary ) {
2243                     histogram_title = "counts difference:";
2244                 }
2245                 else {
2246                     histogram_title = "(maximal) counts difference:";
2247                 }
2248                 break;
2249             case DOMAIN_ID:
2250                 histogram_title = "score mean:";
2251                 break;
2252             case MIN:
2253                 histogram_title = "score minimum:";
2254                 break;
2255             case MAX:
2256                 histogram_title = "score maximum:";
2257                 break;
2258             case MAX_DIFFERENCE:
2259                 if ( treat_as_binary ) {
2260                     histogram_title = "difference:";
2261                 }
2262                 else {
2263                     histogram_title = "(maximal) difference:";
2264                 }
2265                 break;
2266             case MEAN:
2267                 histogram_title = "score mean:";
2268                 break;
2269             case SD:
2270                 histogram_title = "score standard deviation:";
2271                 break;
2272             case SPECIES_COUNT:
2273                 histogram_title = "species number:";
2274                 break;
2275             default:
2276                 throw new AssertionError( "Unknown sort field: " + sort_field );
2277         }
2278         for( final DomainSimilarity similarity : similarities ) {
2279             switch ( sort_field ) {
2280                 case ABS_MAX_COUNTS_DIFFERENCE:
2281                     stats.addValue( Math.abs( similarity.getMaximalDifferenceInCounts() ) );
2282                     break;
2283                 case MAX_COUNTS_DIFFERENCE:
2284                     stats.addValue( similarity.getMaximalDifferenceInCounts() );
2285                     break;
2286                 case DOMAIN_ID:
2287                     stats.addValue( similarity.getMeanSimilarityScore() );
2288                     break;
2289                 case MIN:
2290                     stats.addValue( similarity.getMinimalSimilarityScore() );
2291                     break;
2292                 case MAX:
2293                     stats.addValue( similarity.getMaximalSimilarityScore() );
2294                     break;
2295                 case MAX_DIFFERENCE:
2296                     stats.addValue( similarity.getMaximalDifference() );
2297                     break;
2298                 case MEAN:
2299                     stats.addValue( similarity.getMeanSimilarityScore() );
2300                     break;
2301                 case SD:
2302                     stats.addValue( similarity.getStandardDeviationOfSimilarityScore() );
2303                     break;
2304                 case SPECIES_COUNT:
2305                     stats.addValue( similarity.getSpecies().size() );
2306                     break;
2307                 default:
2308                     throw new AssertionError( "Unknown sort field: " + sort_field );
2309             }
2310         }
2311         //
2312         // final HistogramData[] hists = new HistogramData[ 1 ];
2313         //
2314         //
2315         // List<HistogramDataItem> data_items = new
2316         // ArrayList<HistogramDataItem>();
2317         // double[] values = stats.getDataAsDoubleArray();
2318         // for( int i = 0; i < values.length; i++ ) {
2319         // HistogramDataItem data_item = new BasicHistogramDataItem( "", values[
2320         // i ] );
2321         // data_items.add( data_item );
2322         // }
2323         //
2324         //
2325         // HistogramData hd0 = new HistogramData( "name",
2326         // data_items,
2327         // null, 20,
2328         // 40 );
2329         //
2330         //
2331         //
2332         //
2333         // hists[ 0 ] = hd0;
2334         //
2335         // final HistogramsFrame hf = new HistogramsFrame( hists );
2336         // hf.setVisible( true );
2337         //
2338         AsciiHistogram histo = null;
2339         if ( stats.getMin() < stats.getMin() ) {
2340             histo = new AsciiHistogram( stats, histogram_title );
2341         }
2342         if ( verbose ) {
2343             if ( histo != null ) {
2344                 System.out.println( histo.toStringBuffer( 20, '|', 40, 5 ) );
2345             }
2346             System.out.println();
2347             System.out.println( "N                   : " + stats.getN() );
2348             System.out.println( "Min                 : " + stats.getMin() );
2349             System.out.println( "Max                 : " + stats.getMax() );
2350             System.out.println( "Mean                : " + stats.arithmeticMean() );
2351             if ( stats.getN() > 1 ) {
2352                 System.out.println( "SD                  : " + stats.sampleStandardDeviation() );
2353             }
2354             else {
2355                 System.out.println( "SD                  : n/a" );
2356             }
2357             System.out.println( "Median              : " + stats.median() );
2358             if ( stats.getN() > 1 ) {
2359                 System.out.println( "Pearsonian skewness : " + stats.pearsonianSkewness() );
2360             }
2361             else {
2362                 System.out.println( "Pearsonian skewness : n/a" );
2363             }
2364         }
2365         if ( ( single_writer != null ) && ( ( split_writers == null ) || split_writers.isEmpty() ) ) {
2366             split_writers = new HashMap<Character, Writer>();
2367             split_writers.put( '_', single_writer );
2368         }
2369         switch ( print_option ) {
2370             case SIMPLE_TAB_DELIMITED:
2371                 break;
2372             case HTML:
2373                 for( final Character key : split_writers.keySet() ) {
2374                     final Writer w = split_writers.get( key );
2375                     w.write( "<html>" );
2376                     w.write( SurfacingConstants.NL );
2377                     if ( key != '_' ) {
2378                         addHtmlHead( w, "DCs (" + html_title + ") " + key.toString().toUpperCase() );
2379                     }
2380                     else {
2381                         addHtmlHead( w, "DCs (" + html_title + ")" );
2382                     }
2383                     w.write( SurfacingConstants.NL );
2384                     w.write( "<body>" );
2385                     w.write( SurfacingConstants.NL );
2386                     w.write( html_desc.toString() );
2387                     w.write( SurfacingConstants.NL );
2388                     w.write( "<hr>" );
2389                     w.write( "<br>" );
2390                     w.write( SurfacingConstants.NL );
2391                     w.write( "<tt><pre>" );
2392                     w.write( SurfacingConstants.NL );
2393                     if ( histo != null ) {
2394                         w.write( histo.toStringBuffer( 20, '|', 40, 5 ).toString() );
2395                         w.write( SurfacingConstants.NL );
2396                     }
2397                     w.write( "</pre></tt>" );
2398                     w.write( SurfacingConstants.NL );
2399                     w.write( "<table>" );
2400                     w.write( SurfacingConstants.NL );
2401                     w.write( "<tr><td>N: </td><td>" + stats.getN() + "</td></tr>" );
2402                     w.write( SurfacingConstants.NL );
2403                     w.write( "<tr><td>Min: </td><td>" + stats.getMin() + "</td></tr>" );
2404                     w.write( SurfacingConstants.NL );
2405                     w.write( "<tr><td>Max: </td><td>" + stats.getMax() + "</td></tr>" );
2406                     w.write( SurfacingConstants.NL );
2407                     w.write( "<tr><td>Mean: </td><td>" + stats.arithmeticMean() + "</td></tr>" );
2408                     w.write( SurfacingConstants.NL );
2409                     if ( stats.getN() > 1 ) {
2410                         w.write( "<tr><td>SD: </td><td>" + stats.sampleStandardDeviation() + "</td></tr>" );
2411                     }
2412                     else {
2413                         w.write( "<tr><td>SD: </td><td>n/a</td></tr>" );
2414                     }
2415                     w.write( SurfacingConstants.NL );
2416                     w.write( "<tr><td>Median: </td><td>" + stats.median() + "</td></tr>" );
2417                     w.write( SurfacingConstants.NL );
2418                     if ( stats.getN() > 1 ) {
2419                         w.write( "<tr><td>Pearsonian skewness: </td><td>" + stats.pearsonianSkewness() + "</td></tr>" );
2420                     }
2421                     else {
2422                         w.write( "<tr><td>Pearsonian skewness: </td><td>n/a</td></tr>" );
2423                     }
2424                     w.write( SurfacingConstants.NL );
2425                     w.write( "</table>" );
2426                     w.write( SurfacingConstants.NL );
2427                     w.write( "<br>" );
2428                     w.write( SurfacingConstants.NL );
2429                     w.write( "<hr>" );
2430                     w.write( SurfacingConstants.NL );
2431                     w.write( "<br>" );
2432                     w.write( SurfacingConstants.NL );
2433                     w.write( "<table>" );
2434                     w.write( SurfacingConstants.NL );
2435                 }
2436                 break;
2437         }
2438         for( final Writer w : split_writers.values() ) {
2439             w.write( SurfacingConstants.NL );
2440         }
2441         for( final DomainSimilarity similarity : similarities ) {
2442             if ( ( species_order != null ) && !species_order.isEmpty() ) {
2443                 ( ( PrintableDomainSimilarity ) similarity ).setSpeciesOrder( species_order );
2444             }
2445             if ( single_writer != null ) {
2446                 single_writer.write( similarity.toStringBuffer( print_option ).toString() );
2447             }
2448             else {
2449                 Writer local_writer = split_writers.get( ( similarity.getDomainId().getId().charAt( 0 ) + "" )
2450                         .toLowerCase().charAt( 0 ) );
2451                 if ( local_writer == null ) {
2452                     local_writer = split_writers.get( '0' );
2453                 }
2454                 local_writer.write( similarity.toStringBuffer( print_option ).toString() );
2455             }
2456             for( final Writer w : split_writers.values() ) {
2457                 w.write( SurfacingConstants.NL );
2458             }
2459         }
2460         switch ( print_option ) {
2461             case HTML:
2462                 for( final Writer w : split_writers.values() ) {
2463                     w.write( SurfacingConstants.NL );
2464                     w.write( "</table>" );
2465                     w.write( SurfacingConstants.NL );
2466                     w.write( "</font>" );
2467                     w.write( SurfacingConstants.NL );
2468                     w.write( "</body>" );
2469                     w.write( SurfacingConstants.NL );
2470                     w.write( "</html>" );
2471                     w.write( SurfacingConstants.NL );
2472                 }
2473                 break;
2474         }
2475         for( final Writer w : split_writers.values() ) {
2476             w.close();
2477         }
2478         return stats;
2479     }
2480
2481     private static void writeDomainsToIndividualFilePerTreeNode( final Writer individual_files_writer,
2482                                                                  final String domain_0,
2483                                                                  final String domain_1 ) throws IOException {
2484         individual_files_writer.write( domain_0 );
2485         individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2486         if ( !ForesterUtil.isEmpty( domain_1 ) ) {
2487             individual_files_writer.write( domain_1 );
2488             individual_files_writer.write( ForesterUtil.LINE_SEPARATOR );
2489         }
2490     }
2491
2492     public static void writeMatrixToFile( final CharacterStateMatrix<?> matrix,
2493                                           final String filename,
2494                                           final Format format ) {
2495         final File outfile = new File( filename );
2496         checkForOutputFileWriteability( outfile );
2497         try {
2498             final BufferedWriter out = new BufferedWriter( new FileWriter( outfile ) );
2499             matrix.toWriter( out, format );
2500             out.flush();
2501             out.close();
2502         }
2503         catch ( final IOException e ) {
2504             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2505         }
2506         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote matrix: \"" + filename + "\"" );
2507     }
2508
2509     public static void writeMatrixToFile( final File matrix_outfile, final List<DistanceMatrix> matrices ) {
2510         checkForOutputFileWriteability( matrix_outfile );
2511         try {
2512             final BufferedWriter out = new BufferedWriter( new FileWriter( matrix_outfile ) );
2513             for( final DistanceMatrix distance_matrix : matrices ) {
2514                 out.write( distance_matrix.toStringBuffer( DistanceMatrix.Format.PHYLIP ).toString() );
2515                 out.write( ForesterUtil.LINE_SEPARATOR );
2516                 out.flush();
2517             }
2518             out.close();
2519         }
2520         catch ( final IOException e ) {
2521             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2522         }
2523         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote distance matrices to \"" + matrix_outfile + "\"" );
2524     }
2525
2526     private static void writePfamsToFile( final String outfile_name, final SortedSet<String> pfams ) {
2527         try {
2528             final Writer writer = new BufferedWriter( new FileWriter( new File( outfile_name ) ) );
2529             for( final String pfam : pfams ) {
2530                 writer.write( pfam );
2531                 writer.write( ForesterUtil.LINE_SEPARATOR );
2532             }
2533             writer.close();
2534             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote " + pfams.size() + " pfams to [" + outfile_name
2535                     + "]" );
2536         }
2537         catch ( final IOException e ) {
2538             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "Failure to write: " + e );
2539         }
2540     }
2541
2542     public static void writePhylogenyToFile( final Phylogeny phylogeny, final String filename ) {
2543         final PhylogenyWriter writer = new PhylogenyWriter();
2544         try {
2545             writer.toPhyloXML( new File( filename ), phylogeny, 1 );
2546         }
2547         catch ( final IOException e ) {
2548             ForesterUtil.printWarningMessage( surfacing.PRG_NAME, "failed to write phylogeny to \"" + filename + "\": "
2549                     + e );
2550         }
2551         ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote phylogeny to \"" + filename + "\"" );
2552     }
2553
2554     public static void writeTaxonomyLinks( final Writer writer, final String species ) throws IOException {
2555         if ( ( species.length() > 1 ) && ( species.indexOf( '_' ) < 1 ) ) {
2556             final Matcher matcher = PATTERN_SP_STYLE_TAXONOMY.matcher( species );
2557             writer.write( " [" );
2558             if ( matcher.matches() ) {
2559                 writer.write( "<a href=\"" + SurfacingConstants.UNIPROT_LINK + species
2560                         + "\" target=\"taxonomy_window\">uniprot</a>" );
2561             }
2562             else {
2563                 writer.write( "<a href=\"" + SurfacingConstants.EOL_LINK + species
2564                         + "\" target=\"taxonomy_window\">eol</a>" );
2565                 writer.write( "|" );
2566                 writer.write( "<a href=\"" + SurfacingConstants.TOL_LINK + species
2567                         + "\" target=\"taxonomy_window\">tol</a>" );
2568             }
2569             writer.write( "]" );
2570         }
2571     }
2572
2573     private static void writeToNexus( final String outfile_name,
2574                                       final CharacterStateMatrix<BinaryStates> matrix,
2575                                       final Phylogeny phylogeny ) {
2576         if ( !( matrix instanceof BasicCharacterStateMatrix ) ) {
2577             throw new IllegalArgumentException( "can only write matrices of type [" + BasicCharacterStateMatrix.class
2578                     + "] to nexus" );
2579         }
2580         final BasicCharacterStateMatrix<BinaryStates> my_matrix = ( org.forester.evoinference.matrix.character.BasicCharacterStateMatrix<BinaryStates> ) matrix;
2581         final List<Phylogeny> phylogenies = new ArrayList<Phylogeny>( 1 );
2582         phylogenies.add( phylogeny );
2583         try {
2584             final BufferedWriter w = new BufferedWriter( new FileWriter( outfile_name ) );
2585             w.write( NexusConstants.NEXUS );
2586             w.write( ForesterUtil.LINE_SEPARATOR );
2587             my_matrix.writeNexusTaxaBlock( w );
2588             my_matrix.writeNexusBinaryChractersBlock( w );
2589             PhylogenyWriter.writeNexusTreesBlock( w, phylogenies, NH_CONVERSION_SUPPORT_VALUE_STYLE.NONE );
2590             w.flush();
2591             w.close();
2592             ForesterUtil.programMessage( surfacing.PRG_NAME, "Wrote Nexus file: \"" + outfile_name + "\"" );
2593         }
2594         catch ( final IOException e ) {
2595             ForesterUtil.fatalError( surfacing.PRG_NAME, e.getMessage() );
2596         }
2597     }
2598
2599     private static void writeToNexus( final String outfile_name,
2600                                       final DomainParsimonyCalculator domain_parsimony,
2601                                       final Phylogeny phylogeny ) {
2602         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAINS,
2603                       domain_parsimony.createMatrixOfDomainPresenceOrAbsence(),
2604                       phylogeny );
2605         writeToNexus( outfile_name + surfacing.NEXUS_EXTERNAL_DOMAIN_COMBINATIONS,
2606                       domain_parsimony.createMatrixOfBinaryDomainCombinationPresenceOrAbsence(),
2607                       phylogeny );
2608     }
2609
2610     public static void domainsPerProteinsStatistics( final String genome,
2611                                                      final List<Protein> protein_list,
2612                                                      final DescriptiveStatistics all_genomes_domains_per_potein_stats,
2613                                                      final SortedMap<Integer, Integer> all_genomes_domains_per_potein_histo,
2614                                                      final SortedSet<String> domains_which_are_always_single,
2615                                                      final SortedSet<String> domains_which_are_sometimes_single_sometimes_not,
2616                                                      final SortedSet<String> domains_which_never_single,
2617                                                      final Writer writer ) {
2618         final DescriptiveStatistics stats = new BasicDescriptiveStatistics();
2619         for( final Protein protein : protein_list ) {
2620             final int domains = protein.getNumberOfProteinDomains();
2621             //System.out.println( domains );
2622             stats.addValue( domains );
2623             all_genomes_domains_per_potein_stats.addValue( domains );
2624             if ( !all_genomes_domains_per_potein_histo.containsKey( domains ) ) {
2625                 all_genomes_domains_per_potein_histo.put( domains, 1 );
2626             }
2627             else {
2628                 all_genomes_domains_per_potein_histo.put( domains,
2629                                                           1 + all_genomes_domains_per_potein_histo.get( domains ) );
2630             }
2631             if ( domains == 1 ) {
2632                 final String domain = protein.getProteinDomain( 0 ).getDomainId().getId();
2633                 if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2634                     if ( domains_which_never_single.contains( domain ) ) {
2635                         domains_which_never_single.remove( domain );
2636                         domains_which_are_sometimes_single_sometimes_not.add( domain );
2637                     }
2638                     else {
2639                         domains_which_are_always_single.add( domain );
2640                     }
2641                 }
2642             }
2643             else if ( domains > 1 ) {
2644                 for( final Domain d : protein.getProteinDomains() ) {
2645                     final String domain = d.getDomainId().getId();
2646                     // System.out.println( domain );
2647                     if ( !domains_which_are_sometimes_single_sometimes_not.contains( domain ) ) {
2648                         if ( domains_which_are_always_single.contains( domain ) ) {
2649                             domains_which_are_always_single.remove( domain );
2650                             domains_which_are_sometimes_single_sometimes_not.add( domain );
2651                         }
2652                         else {
2653                             domains_which_never_single.add( domain );
2654                         }
2655                     }
2656                 }
2657             }
2658         }
2659         try {
2660             writer.write( genome );
2661             writer.write( "\t" );
2662             if ( stats.getN() >= 1 ) {
2663                 writer.write( stats.arithmeticMean() + "" );
2664                 writer.write( "\t" );
2665                 if ( stats.getN() >= 2 ) {
2666                     writer.write( stats.sampleStandardDeviation() + "" );
2667                 }
2668                 else {
2669                     writer.write( "" );
2670                 }
2671                 writer.write( "\t" );
2672                 writer.write( stats.median() + "" );
2673                 writer.write( "\t" );
2674                 writer.write( stats.getN() + "" );
2675                 writer.write( "\t" );
2676                 writer.write( stats.getMin() + "" );
2677                 writer.write( "\t" );
2678                 writer.write( stats.getMax() + "" );
2679             }
2680             else {
2681                 writer.write( "\t" );
2682                 writer.write( "\t" );
2683                 writer.write( "\t" );
2684                 writer.write( "0" );
2685                 writer.write( "\t" );
2686                 writer.write( "\t" );
2687             }
2688             writer.write( "\n" );
2689         }
2690         catch ( final IOException e ) {
2691             e.printStackTrace();
2692         }
2693     }
2694
2695     final static class DomainComparator implements Comparator<Domain> {
2696
2697         final private boolean _ascending;
2698
2699         public DomainComparator( final boolean ascending ) {
2700             _ascending = ascending;
2701         }
2702
2703         @Override
2704         public final int compare( final Domain d0, final Domain d1 ) {
2705             if ( d0.getFrom() < d1.getFrom() ) {
2706                 return _ascending ? -1 : 1;
2707             }
2708             else if ( d0.getFrom() > d1.getFrom() ) {
2709                 return _ascending ? 1 : -1;
2710             }
2711             return 0;
2712         }
2713     }
2714 }