forester/java/src/org/forester/surfacing/PrintableDomainSimilarity.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.util.List;
  30 import java.util.Map;
  31 import java.util.SortedMap;
  32 import java.util.SortedSet;
  33 import java.util.TreeSet;
  34
  35 import org.forester.go.GoId;
  36 import org.forester.go.GoNameSpace;
  37 import org.forester.go.GoTerm;
  38 import org.forester.go.GoXRef;
  39 import org.forester.protein.DomainId;
  40 import org.forester.species.Species;
  41 import org.forester.surfacing.DomainSimilarityCalculator.Detailedness;
  42 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  43 import org.forester.util.ForesterUtil;
  44
  45 public class PrintableDomainSimilarity implements DomainSimilarity {
  46
  47     final public static String                                           SPECIES_SEPARATOR = "  ";
  48     final private static char                                            TAB               = '\t';
  49     final private static int                                             BEFORE            = -1;
  50     final private static int                                             EQUAL             = 0;
  51     final private static int                                             AFTER             = 1;
  52     final private static String                                          NO_SPECIES        = "     ";
  53     final private double                                                 _min;
  54     final private double                                                 _max;
  55     final private double                                                 _mean;
  56     final private double                                                 _sd;
  57     final private int                                                    _n;
  58     private final int                                                    _max_difference_in_counts;
  59     private final int                                                    _max_difference;
  60     private DomainSimilarityCalculator.GoAnnotationOutput                _go_annotation_output;
  61     final private CombinableDomains                                      _combinable_domains;
  62     final private SortedMap<Species, SpeciesSpecificDomainSimilariyData> _species_data;
  63     final private DomainSimilaritySortField                              _sort_field;
  64     private List<Species>                                                _species_order;
  65     private final boolean                                                _sort_by_species_count_first;
  66     private DomainSimilarityCalculator.Detailedness                      _detailedness;
  67     private Map<GoId, GoTerm>                                            _go_id_to_term_map;
  68     private GoNameSpace                                                  _go_namespace_limit;
  69     private final boolean                                                _treat_as_binary_comparison;
  70
  71     /**
  72      * If go_id_to_term_map not null, detailed GO information is written,
  73      * only GO ids otherwise.
  74      *
  75      *
  76      */
  77     public PrintableDomainSimilarity( final CombinableDomains combinable_domains,
  78                                       final double min,
  79                                       final double max,
  80                                       final double mean,
  81                                       final double median,
  82                                       final double sd,
  83                                       final int n,
  84                                       final int max_difference_in_counts,
  85                                       final int max_difference,
  86                                       final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data,
  87                                       final DomainSimilaritySortField sort_field,
  88                                       final boolean sort_by_species_count_first,
  89                                       final boolean treat_as_binary_comparison ) {
  90         if ( combinable_domains == null ) {
  91             throw new IllegalArgumentException( "attempt to use null combinable domains" );
  92         }
  93         if ( sort_field == null ) {
  94             throw new IllegalArgumentException( "attempt to use null sorting" );
  95         }
  96         if ( species_data == null ) {
  97             throw new IllegalArgumentException( "attempt to use null species data" );
  98         }
  99         if ( species_data.size() < 1 ) {
 100             throw new IllegalArgumentException( "attempt to use empty species data" );
 101         }
 102         if ( n < 0 ) {
 103             throw new IllegalArgumentException( "attempt to use N less than 0" );
 104         }
 105         if ( ( species_data.size() > 1 ) && ( n < 1 ) ) {
 106             throw new IllegalArgumentException( "attempt to use N less than 1" );
 107         }
 108         if ( sd < 0.0 ) {
 109             throw new IllegalArgumentException( "attempt to use negative SD" );
 110         }
 111         if ( max < min ) {
 112             throw new IllegalArgumentException( "attempt to use max smaller than min" );
 113         }
 114         init();
 115         _combinable_domains = combinable_domains;
 116         _min = min;
 117         _max = max;
 118         _mean = mean;
 119         _sd = sd;
 120         _n = n;
 121         _max_difference_in_counts = max_difference_in_counts;
 122         _max_difference = max_difference;
 123         _species_data = species_data;
 124         _sort_field = sort_field;
 125         _sort_by_species_count_first = sort_by_species_count_first;
 126         _treat_as_binary_comparison = treat_as_binary_comparison;
 127         final int s = species_data.size();
 128         if ( ( ( s * s ) - s ) != ( getN() * 2 ) ) {
 129             throw new IllegalArgumentException( "illegal species count and n: species count:" + s + ", n:" + _n
 130                     + " for domain " + combinable_domains.getKeyDomain() );
 131         }
 132         if ( s > 2 ) {
 133             if ( getMaximalDifferenceInCounts() < 0 ) {
 134                 throw new IllegalArgumentException( "attempt to use negative max difference in counts with more than two species" );
 135             }
 136             if ( getMaximalDifference() < 0 ) {
 137                 throw new IllegalArgumentException( "attempt to use negative max difference with more than two species" );
 138             }
 139         }
 140     }
 141
 142     private void addGoInformation( final StringBuffer sb, final boolean for_table, final boolean html ) {
 143         if ( !for_table ) {
 144             sb.append( "<" );
 145         }
 146         switch ( getGoAnnotationOutput() ) {
 147             case ALL: {
 148                 final int go_ids = getCombinableDomains().getKeyDomain().getNumberOfGoIds();
 149                 boolean first = true;
 150                 for( int i = 0; i < go_ids; ++i ) {
 151                     final GoId go_id = getCombinableDomains().getKeyDomain().getGoId( i );
 152                     if ( getGoIdToTermMap() != null ) {
 153                         if ( getGoIdToTermMap().containsKey( go_id ) ) {
 154                             first = appendGoTerm( sb, getGoIdToTermMap().get( go_id ), first, html );
 155                         }
 156                         else {
 157                             sb.append( "go id \"" + go_id + "\" not found ["
 158                                     + getCombinableDomains().getKeyDomain().getId() + "]" );
 159                         }
 160                     }
 161                     else {
 162                         if ( !first ) {
 163                             sb.append( ", " );
 164                         }
 165                         if ( html ) {
 166                             sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id
 167                                     + "\" target=\"amigo_window\">" + go_id + "</a>" );
 168                         }
 169                         else {
 170                             sb.append( go_id );
 171                         }
 172                         first = false;
 173                     }
 174                 }
 175                 break;
 176             }
 177             case NONE: {
 178                 break;
 179             }
 180             default:
 181                 throw new RuntimeException( "unknown " + getGoAnnotationOutput() );
 182         }
 183         if ( !for_table ) {
 184             sb.append( ">: " );
 185         }
 186     }
 187
 188     private void addSpeciesSpecificDomainData( final StringBuffer sb,
 189                                                final Species species,
 190                                                final boolean html,
 191                                                final Map<String, Integer> tax_code_to_id_map ) {
 192         if ( getDetaildness() != DomainSimilarityCalculator.Detailedness.BASIC ) {
 193             sb.append( "[" );
 194         }
 195         if ( html ) {
 196             sb.append( "<b>" );
 197             final String tax_code = species.getSpeciesId();
 198             if ( !ForesterUtil.isEmpty( tax_code )
 199                     && ( ( tax_code_to_id_map != null ) && tax_code_to_id_map.containsKey( tax_code ) ) ) {
 200                 sb.append( "<a href=\"" + SurfacingConstants.UNIPROT_TAXONOMY_ID_LINK
 201                         + tax_code_to_id_map.get( tax_code ) + "\" target=\"taxonomy_window\">" + tax_code + "</a>" );
 202             }
 203             else {
 204                 sb.append( tax_code );
 205             }
 206             sb.append( "</b>" );
 207         }
 208         else {
 209             sb.append( species.getSpeciesId() );
 210         }
 211         if ( getDetaildness() != DomainSimilarityCalculator.Detailedness.BASIC ) {
 212             sb.append( ":" );
 213             sb.append( getSpeciesData().get( species ).toStringBuffer( getDetaildness(), html ) );
 214             sb.append( "]" );
 215         }
 216         if ( html ) {
 217             sb.append( "<br>" );
 218         }
 219         sb.append( PrintableDomainSimilarity.SPECIES_SEPARATOR );
 220     }
 221
 222     private boolean appendGoTerm( final StringBuffer sb, final GoTerm go_term, final boolean first, final boolean html ) {
 223         if ( ( getGoNamespaceLimit() == null ) || getGoNamespaceLimit().equals( go_term.getGoNameSpace() ) ) {
 224             if ( !first ) {
 225                 sb.append( ", " );
 226             }
 227             final GoId go_id = go_term.getGoId();
 228             if ( html ) {
 229                 sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
 230                         + "</a>" );
 231             }
 232             else {
 233                 sb.append( go_id );
 234             }
 235             sb.append( ":" );
 236             sb.append( go_term.getName() );
 237             if ( !html ) {
 238                 if ( getGoNamespaceLimit() == null ) {
 239                     sb.append( ":" );
 240                     sb.append( go_term.getGoNameSpace().toString() );
 241                 }
 242                 for( final GoXRef xref : go_term.getGoXRefs() ) {
 243                     sb.append( ":" );
 244                     sb.append( xref.toString() );
 245                 }
 246             }
 247             return false;
 248         }
 249         return true;
 250     }
 251
 252     private void boldEndIfSortedBy( final DomainSimilaritySortField sort_field, final StringBuffer sb ) {
 253         if ( getSortField() == sort_field ) {
 254             sb.append( "</b>" );
 255         }
 256     }
 257
 258     private void boldStartIfSortedBy( final DomainSimilaritySortField sort_field, final StringBuffer sb ) {
 259         if ( getSortField() == sort_field ) {
 260             sb.append( "<b>" );
 261         }
 262     }
 263
 264     private int compareByDomainId( final DomainSimilarity other ) {
 265         return getDomainId().compareTo( other.getDomainId() );
 266     }
 267
 268     private int compareBySpeciesCount( final DomainSimilarity domain_similarity ) {
 269         final int s_this = getSpeciesData().size();
 270         final int s_other = domain_similarity.getSpeciesData().size();
 271         if ( s_this < s_other ) {
 272             return PrintableDomainSimilarity.BEFORE;
 273         }
 274         else if ( s_this > s_other ) {
 275             return PrintableDomainSimilarity.AFTER;
 276         }
 277         else {
 278             return PrintableDomainSimilarity.EQUAL;
 279         }
 280     }
 281
 282     @Override
 283     public int compareTo( final DomainSimilarity domain_similarity ) {
 284         if ( this == domain_similarity ) {
 285             return PrintableDomainSimilarity.EQUAL;
 286         }
 287         else if ( domain_similarity == null ) {
 288             throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to null" );
 289         }
 290         else if ( domain_similarity.getClass() != this.getClass() ) {
 291             throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to "
 292                     + domain_similarity.getClass() );
 293         }
 294         switch ( getSortField() ) {
 295             case MIN:
 296                 if ( isSortBySpeciesCountFirst() ) {
 297                     final int i = compareBySpeciesCount( domain_similarity );
 298                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 299                         return i;
 300                     }
 301                 }
 302                 if ( getMinimalSimilarityScore() < domain_similarity.getMinimalSimilarityScore() ) {
 303                     return PrintableDomainSimilarity.BEFORE;
 304                 }
 305                 else if ( getMinimalSimilarityScore() > domain_similarity.getMinimalSimilarityScore() ) {
 306                     return PrintableDomainSimilarity.AFTER;
 307                 }
 308                 else {
 309                     return compareByDomainId( domain_similarity );
 310                 }
 311             case MAX:
 312                 if ( isSortBySpeciesCountFirst() ) {
 313                     final int i = compareBySpeciesCount( domain_similarity );
 314                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 315                         return i;
 316                     }
 317                 }
 318                 if ( getMaximalSimilarityScore() < domain_similarity.getMaximalSimilarityScore() ) {
 319                     return PrintableDomainSimilarity.BEFORE;
 320                 }
 321                 else if ( getMaximalSimilarityScore() > domain_similarity.getMaximalSimilarityScore() ) {
 322                     return PrintableDomainSimilarity.AFTER;
 323                 }
 324                 else {
 325                     return compareByDomainId( domain_similarity );
 326                 }
 327             case MEAN:
 328                 if ( isSortBySpeciesCountFirst() ) {
 329                     final int i = compareBySpeciesCount( domain_similarity );
 330                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 331                         return i;
 332                     }
 333                 }
 334                 if ( getMeanSimilarityScore() < domain_similarity.getMeanSimilarityScore() ) {
 335                     return PrintableDomainSimilarity.BEFORE;
 336                 }
 337                 else if ( getMeanSimilarityScore() > domain_similarity.getMeanSimilarityScore() ) {
 338                     return PrintableDomainSimilarity.AFTER;
 339                 }
 340                 else {
 341                     return compareByDomainId( domain_similarity );
 342                 }
 343             case SD:
 344                 if ( isSortBySpeciesCountFirst() ) {
 345                     final int i = compareBySpeciesCount( domain_similarity );
 346                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 347                         return i;
 348                     }
 349                 }
 350                 if ( getStandardDeviationOfSimilarityScore() < domain_similarity
 351                         .getStandardDeviationOfSimilarityScore() ) {
 352                     return PrintableDomainSimilarity.BEFORE;
 353                 }
 354                 else if ( getStandardDeviationOfSimilarityScore() > domain_similarity
 355                         .getStandardDeviationOfSimilarityScore() ) {
 356                     return PrintableDomainSimilarity.AFTER;
 357                 }
 358                 else {
 359                     return compareByDomainId( domain_similarity );
 360                 }
 361             case MAX_DIFFERENCE:
 362                 if ( isSortBySpeciesCountFirst() ) {
 363                     final int i = compareBySpeciesCount( domain_similarity );
 364                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 365                         return i;
 366                     }
 367                 }
 368                 if ( getMaximalDifference() > domain_similarity.getMaximalDifference() ) {
 369                     return PrintableDomainSimilarity.BEFORE;
 370                 }
 371                 else if ( getMaximalDifference() < domain_similarity.getMaximalDifference() ) {
 372                     return PrintableDomainSimilarity.AFTER;
 373                 }
 374                 else {
 375                     return compareByDomainId( domain_similarity );
 376                 }
 377             case ABS_MAX_COUNTS_DIFFERENCE:
 378                 if ( isSortBySpeciesCountFirst() ) {
 379                     final int i = compareBySpeciesCount( domain_similarity );
 380                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 381                         return i;
 382                     }
 383                 }
 384                 if ( Math.abs( getMaximalDifferenceInCounts() ) > Math.abs( domain_similarity
 385                         .getMaximalDifferenceInCounts() ) ) {
 386                     return PrintableDomainSimilarity.BEFORE;
 387                 }
 388                 else if ( Math.abs( getMaximalDifferenceInCounts() ) < Math.abs( domain_similarity
 389                         .getMaximalDifferenceInCounts() ) ) {
 390                     return PrintableDomainSimilarity.AFTER;
 391                 }
 392                 else {
 393                     return compareByDomainId( domain_similarity );
 394                 }
 395             case MAX_COUNTS_DIFFERENCE:
 396                 if ( getSpeciesData().size() != 2 ) {
 397                     throw new RuntimeException( "attempt to sort by maximal difference with species not equal to two" );
 398                 }
 399                 if ( isSortBySpeciesCountFirst() ) {
 400                     final int i = compareBySpeciesCount( domain_similarity );
 401                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 402                         return i;
 403                     }
 404                 }
 405                 if ( getMaximalDifferenceInCounts() > domain_similarity.getMaximalDifferenceInCounts() ) {
 406                     return PrintableDomainSimilarity.BEFORE;
 407                 }
 408                 else if ( getMaximalDifferenceInCounts() < domain_similarity.getMaximalDifferenceInCounts() ) {
 409                     return PrintableDomainSimilarity.AFTER;
 410                 }
 411                 else {
 412                     return compareByDomainId( domain_similarity );
 413                 }
 414             case SPECIES_COUNT:
 415                 final int i = compareBySpeciesCount( domain_similarity );
 416                 if ( i != PrintableDomainSimilarity.EQUAL ) {
 417                     return i;
 418                 }
 419                 else {
 420                     return compareByDomainId( domain_similarity );
 421                 }
 422             case DOMAIN_ID:
 423                 return compareByDomainId( domain_similarity );
 424         }
 425         throw new AssertionError( "Unknown sort method: " + getSortField() );
 426     }
 427
 428     @Override
 429     public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain ) {
 430         final SortedSet<DomainId> sorted_ids = new TreeSet<DomainId>();
 431         if ( getSpeciesData().containsKey( species_of_combinable_domain ) ) {
 432             for( final DomainId id : getSpeciesData().get( species_of_combinable_domain )
 433                     .getCombinableDomainIdToCountsMap().keySet() ) {
 434                 sorted_ids.add( id );
 435             }
 436         }
 437         return sorted_ids;
 438     }
 439
 440     private CombinableDomains getCombinableDomains() {
 441         return _combinable_domains;
 442     }
 443
 444     private DomainSimilarityCalculator.Detailedness getDetaildness() {
 445         return _detailedness;
 446     }
 447
 448     @Override
 449     public DomainId getDomainId() {
 450         return getCombinableDomains().getKeyDomain();
 451     }
 452
 453     private DomainSimilarityCalculator.GoAnnotationOutput getGoAnnotationOutput() {
 454         return _go_annotation_output;
 455     }
 456
 457     private Map<GoId, GoTerm> getGoIdToTermMap() {
 458         return _go_id_to_term_map;
 459     }
 460
 461     public GoNameSpace getGoNamespaceLimit() {
 462         return _go_namespace_limit;
 463     }
 464
 465     @Override
 466     public int getMaximalDifference() {
 467         return _max_difference;
 468     }
 469
 470     @Override
 471     public int getMaximalDifferenceInCounts() {
 472         return _max_difference_in_counts;
 473     }
 474
 475     @Override
 476     public double getMaximalSimilarityScore() {
 477         return _max;
 478     }
 479
 480     @Override
 481     public double getMeanSimilarityScore() {
 482         return _mean;
 483     }
 484
 485     @Override
 486     public double getMinimalSimilarityScore() {
 487         return _min;
 488     }
 489
 490     @Override
 491     public int getN() {
 492         return _n;
 493     }
 494
 495     private DomainSimilaritySortField getSortField() {
 496         return _sort_field;
 497     }
 498
 499     @Override
 500     public SortedSet<Species> getSpecies() {
 501         final SortedSet<Species> species = new TreeSet<Species>();
 502         for( final Species s : getSpeciesData().keySet() ) {
 503             species.add( s );
 504         }
 505         return species;
 506     }
 507
 508     public List<Species> getSpeciesCustomOrder() {
 509         return _species_order;
 510     }
 511
 512     @Override
 513     public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData() {
 514         return _species_data;
 515     }
 516
 517     private StringBuffer getSpeciesDataInAlphabeticalOrder( final boolean html,
 518                                                             final Map<String, Integer> tax_code_to_id_map ) {
 519         final StringBuffer sb = new StringBuffer();
 520         for( final Species species : getSpeciesData().keySet() ) {
 521             addSpeciesSpecificDomainData( sb, species, html, tax_code_to_id_map );
 522         }
 523         return sb;
 524     }
 525
 526     private StringBuffer getSpeciesDataInCustomOrder( final boolean html, final Map<String, Integer> tax_code_to_id_map ) {
 527         final StringBuffer sb = new StringBuffer();
 528         for( final Species order_species : getSpeciesCustomOrder() ) {
 529             if ( getSpeciesData().keySet().contains( order_species ) ) {
 530                 addSpeciesSpecificDomainData( sb, order_species, html, tax_code_to_id_map );
 531             }
 532             else {
 533                 sb.append( PrintableDomainSimilarity.NO_SPECIES );
 534                 sb.append( PrintableDomainSimilarity.SPECIES_SEPARATOR );
 535             }
 536         }
 537         return sb;
 538     }
 539
 540     @Override
 541     public double getStandardDeviationOfSimilarityScore() {
 542         return _sd;
 543     }
 544
 545     private void init() {
 546         _detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 547         _go_annotation_output = null;
 548         _go_id_to_term_map = null;
 549     }
 550
 551     private boolean isSortBySpeciesCountFirst() {
 552         return _sort_by_species_count_first;
 553     }
 554
 555     private boolean isTreatAsBinaryComparison() {
 556         return _treat_as_binary_comparison;
 557     }
 558
 559     public void setDetailedness( final Detailedness detailedness ) {
 560         _detailedness = detailedness;
 561     }
 562
 563     public void setGoAnnotationOutput( final GoAnnotationOutput go_annotation_output ) {
 564         _go_annotation_output = go_annotation_output;
 565     }
 566
 567     public void setGoIdToTermMap( final Map<GoId, GoTerm> go_id_to_term_map ) {
 568         _go_id_to_term_map = go_id_to_term_map;
 569     }
 570
 571     public void setGoNamespaceLimit( final GoNameSpace go_namespace_limit ) {
 572         _go_namespace_limit = go_namespace_limit;
 573     }
 574
 575     public void setSpeciesOrder( final List<Species> species_order ) {
 576         if ( !species_order.containsAll( getSpeciesData().keySet() ) ) {
 577             throw new IllegalArgumentException( "list to order species must contain all species of multiple combinable domains similarity" );
 578         }
 579         _species_order = species_order;
 580     }
 581
 582     @Override
 583     public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option,
 584                                         final Map<String, Integer> tax_code_to_id_map ) {
 585         switch ( print_option ) {
 586             case SIMPLE_TAB_DELIMITED:
 587                 return toStringBufferSimpleTabDelimited();
 588             case HTML:
 589                 return toStringBufferDetailedHTML( tax_code_to_id_map );
 590             default:
 591                 throw new AssertionError( "Unknown print option: " + print_option );
 592         }
 593     }
 594
 595     private StringBuffer toStringBufferDetailedHTML( final Map<String, Integer> tax_code_to_id_map ) {
 596         final StringBuffer sb = new StringBuffer();
 597         sb.append( "<tr>" );
 598         sb.append( "<td>" );
 599         boldStartIfSortedBy( DomainSimilaritySortField.DOMAIN_ID, sb );
 600         sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + getDomainId() + "\" target=\"pfam_window\">"
 601                 + getDomainId() + "</a>" );
 602         boldEndIfSortedBy( DomainSimilaritySortField.DOMAIN_ID, sb );
 603         sb.append( "</td>" );
 604         sb.append( "<td>" );
 605         sb.append( "<a href=\"" + SurfacingConstants.GOOGLE_SCHOLAR_SEARCH + getDomainId()
 606                 + "\" target=\"gs_window\">gs</a>" );
 607         sb.append( "</td>" );
 608         sb.append( "<td>" );
 609         boldStartIfSortedBy( DomainSimilaritySortField.MEAN, sb );
 610         sb.append( ForesterUtil.round( getMeanSimilarityScore(), 3 ) );
 611         boldEndIfSortedBy( DomainSimilaritySortField.MEAN, sb );
 612         sb.append( "</td>" );
 613         if ( !isTreatAsBinaryComparison() ) {
 614             sb.append( "<td>" );
 615             sb.append( "(" );
 616             boldStartIfSortedBy( DomainSimilaritySortField.SD, sb );
 617             sb.append( ForesterUtil.round( getStandardDeviationOfSimilarityScore(), 3 ) );
 618             boldEndIfSortedBy( DomainSimilaritySortField.SD, sb );
 619             sb.append( ")" );
 620             sb.append( "</td>" );
 621             sb.append( "<td>" );
 622             sb.append( "[" );
 623             boldStartIfSortedBy( DomainSimilaritySortField.MIN, sb );
 624             sb.append( ForesterUtil.round( getMinimalSimilarityScore(), 3 ) );
 625             boldEndIfSortedBy( DomainSimilaritySortField.MIN, sb );
 626             sb.append( "," );
 627             boldStartIfSortedBy( DomainSimilaritySortField.MAX, sb );
 628             sb.append( ForesterUtil.round( getMaximalSimilarityScore(), 3 ) );
 629             boldEndIfSortedBy( DomainSimilaritySortField.MAX, sb );
 630             sb.append( "]" );
 631             sb.append( "</td>" );
 632         }
 633         sb.append( "<td>" );
 634         boldStartIfSortedBy( DomainSimilaritySortField.MAX_DIFFERENCE, sb );
 635         sb.append( getMaximalDifference() );
 636         boldEndIfSortedBy( DomainSimilaritySortField.MAX_DIFFERENCE, sb );
 637         sb.append( "</td>" );
 638         sb.append( "<td>" );
 639         if ( isTreatAsBinaryComparison() ) {
 640             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 641             boldStartIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 642             sb.append( getMaximalDifferenceInCounts() );
 643             boldEndIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 644             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 645         }
 646         else {
 647             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 648             boldStartIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 649             sb.append( Math.abs( getMaximalDifferenceInCounts() ) );
 650             boldEndIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 651             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 652         }
 653         sb.append( "</td>" );
 654         if ( !isTreatAsBinaryComparison() ) {
 655             sb.append( "<td>" );
 656             if ( ( getSortField() == DomainSimilaritySortField.SPECIES_COUNT ) || isSortBySpeciesCountFirst() ) {
 657                 sb.append( "<b>" );
 658             }
 659             sb.append( getSpeciesData().size() );
 660             if ( ( getSortField() == DomainSimilaritySortField.SPECIES_COUNT ) || isSortBySpeciesCountFirst() ) {
 661                 sb.append( "</b>" );
 662             }
 663             sb.append( "</td>" );
 664         }
 665         if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
 666             sb.append( "<td>" );
 667             addGoInformation( sb, true, true );
 668             sb.append( "</td>" );
 669         }
 670         if ( ( getSpeciesCustomOrder() == null ) || getSpeciesCustomOrder().isEmpty() ) {
 671             sb.append( "<td>" );
 672             sb.append( getSpeciesDataInAlphabeticalOrder( true, tax_code_to_id_map ) );
 673             sb.append( "</td>" );
 674         }
 675         else {
 676             sb.append( "<td>" );
 677             sb.append( getSpeciesDataInCustomOrder( true, tax_code_to_id_map ) );
 678             sb.append( "</td>" );
 679         }
 680         sb.append( "</tr>" );
 681         return sb;
 682     }
 683
 684     private StringBuffer toStringBufferSimpleTabDelimited() {
 685         final StringBuffer sb = new StringBuffer();
 686         sb.append( getDomainId() );
 687         switch ( getSortField() ) {
 688             case MIN:
 689                 sb.append( TAB );
 690                 sb.append( ForesterUtil.round( getMinimalSimilarityScore(), 3 ) );
 691                 break;
 692             case MAX:
 693                 sb.append( TAB );
 694                 sb.append( ForesterUtil.round( getMaximalSimilarityScore(), 3 ) );
 695                 break;
 696             case MEAN:
 697                 sb.append( TAB );
 698                 sb.append( ForesterUtil.round( getMeanSimilarityScore(), 3 ) );
 699                 break;
 700             case SD:
 701                 sb.append( TAB );
 702                 sb.append( ForesterUtil.round( getStandardDeviationOfSimilarityScore(), 3 ) );
 703                 break;
 704             case MAX_DIFFERENCE:
 705                 sb.append( TAB );
 706                 sb.append( getMaximalDifference() );
 707             case ABS_MAX_COUNTS_DIFFERENCE:
 708             case MAX_COUNTS_DIFFERENCE:
 709                 sb.append( TAB );
 710                 if ( isTreatAsBinaryComparison() ) {
 711                     sb.append( getMaximalDifferenceInCounts() );
 712                 }
 713                 else {
 714                     sb.append( Math.abs( getMaximalDifferenceInCounts() ) );
 715                 }
 716                 break;
 717             case SPECIES_COUNT:
 718                 sb.append( TAB );
 719                 sb.append( getSpeciesData().size() );
 720                 break;
 721             case DOMAIN_ID:
 722                 break;
 723             default:
 724                 throw new AssertionError( "Unknown sort method: " + getSortField() );
 725         }
 726         if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
 727             sb.append( TAB );
 728             addGoInformation( sb, true, false );
 729         }
 730         return sb;
 731     }
 732
 733     public static enum PRINT_OPTION {
 734         SIMPLE_TAB_DELIMITED, HTML;
 735     }
 736 }