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: www.phylosoft.org/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, final Species species, final boolean html ) {
 189         if ( getDetaildness() != DomainSimilarityCalculator.Detailedness.BASIC ) {
 190             sb.append( "[" );
 191         }
 192         if ( html ) {
 193             sb.append( "<b>" );
 194             if ( ( SurfacingConstants.TAXONOMY_LINK != null ) && ( species.getSpeciesId().length() > 2 )
 195                     && ( species.getSpeciesId().length() < 6 ) ) {
 196                 sb.append( "<a href=\"" + SurfacingConstants.TAXONOMY_LINK + species.getSpeciesId()
 197                         + "\" target=\"taxonomy_window\">" + species.getSpeciesId() + "</a>" );
 198             }
 199             else {
 200                 sb.append( species.getSpeciesId() );
 201             }
 202             sb.append( "</b>" );
 203         }
 204         else {
 205             sb.append( species.getSpeciesId() );
 206         }
 207         if ( getDetaildness() != DomainSimilarityCalculator.Detailedness.BASIC ) {
 208             sb.append( ":" );
 209             sb.append( getSpeciesData().get( species ).toStringBuffer( getDetaildness(), html ) );
 210             sb.append( "]" );
 211         }
 212         if ( html ) {
 213             sb.append( "<br>" );
 214         }
 215         sb.append( PrintableDomainSimilarity.SPECIES_SEPARATOR );
 216     }
 217
 218     private boolean appendGoTerm( final StringBuffer sb, final GoTerm go_term, final boolean first, final boolean html ) {
 219         if ( ( getGoNamespaceLimit() == null ) || getGoNamespaceLimit().equals( go_term.getGoNameSpace() ) ) {
 220             if ( !first ) {
 221                 sb.append( ", " );
 222             }
 223             final GoId go_id = go_term.getGoId();
 224             if ( html ) {
 225                 sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
 226                         + "</a>" );
 227             }
 228             else {
 229                 sb.append( go_id );
 230             }
 231             sb.append( ":" );
 232             sb.append( go_term.getName() );
 233             if ( !html ) {
 234                 if ( getGoNamespaceLimit() == null ) {
 235                     sb.append( ":" );
 236                     sb.append( go_term.getGoNameSpace().toString() );
 237                 }
 238                 for( final GoXRef xref : go_term.getGoXRefs() ) {
 239                     sb.append( ":" );
 240                     sb.append( xref.toString() );
 241                 }
 242             }
 243             return false;
 244         }
 245         return true;
 246     }
 247
 248     private void boldEndIfSortedBy( final DomainSimilaritySortField sort_field, final StringBuffer sb ) {
 249         if ( getSortField() == sort_field ) {
 250             sb.append( "</b>" );
 251         }
 252     }
 253
 254     private void boldStartIfSortedBy( final DomainSimilaritySortField sort_field, final StringBuffer sb ) {
 255         if ( getSortField() == sort_field ) {
 256             sb.append( "<b>" );
 257         }
 258     }
 259
 260     private int compareByDomainId( final DomainSimilarity other ) {
 261         return getDomainId().compareTo( other.getDomainId() );
 262     }
 263
 264     private int compareBySpeciesCount( final DomainSimilarity domain_similarity ) {
 265         final int s_this = getSpeciesData().size();
 266         final int s_other = domain_similarity.getSpeciesData().size();
 267         if ( s_this < s_other ) {
 268             return PrintableDomainSimilarity.BEFORE;
 269         }
 270         else if ( s_this > s_other ) {
 271             return PrintableDomainSimilarity.AFTER;
 272         }
 273         else {
 274             return PrintableDomainSimilarity.EQUAL;
 275         }
 276     }
 277
 278     @Override
 279     public int compareTo( final DomainSimilarity domain_similarity ) {
 280         if ( this == domain_similarity ) {
 281             return PrintableDomainSimilarity.EQUAL;
 282         }
 283         else if ( domain_similarity == null ) {
 284             throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to null" );
 285         }
 286         else if ( domain_similarity.getClass() != this.getClass() ) {
 287             throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to "
 288                     + domain_similarity.getClass() );
 289         }
 290         switch ( getSortField() ) {
 291             case MIN:
 292                 if ( isSortBySpeciesCountFirst() ) {
 293                     final int i = compareBySpeciesCount( domain_similarity );
 294                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 295                         return i;
 296                     }
 297                 }
 298                 if ( getMinimalSimilarityScore() < domain_similarity.getMinimalSimilarityScore() ) {
 299                     return PrintableDomainSimilarity.BEFORE;
 300                 }
 301                 else if ( getMinimalSimilarityScore() > domain_similarity.getMinimalSimilarityScore() ) {
 302                     return PrintableDomainSimilarity.AFTER;
 303                 }
 304                 else {
 305                     return compareByDomainId( domain_similarity );
 306                 }
 307             case MAX:
 308                 if ( isSortBySpeciesCountFirst() ) {
 309                     final int i = compareBySpeciesCount( domain_similarity );
 310                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 311                         return i;
 312                     }
 313                 }
 314                 if ( getMaximalSimilarityScore() < domain_similarity.getMaximalSimilarityScore() ) {
 315                     return PrintableDomainSimilarity.BEFORE;
 316                 }
 317                 else if ( getMaximalSimilarityScore() > domain_similarity.getMaximalSimilarityScore() ) {
 318                     return PrintableDomainSimilarity.AFTER;
 319                 }
 320                 else {
 321                     return compareByDomainId( domain_similarity );
 322                 }
 323             case MEAN:
 324                 if ( isSortBySpeciesCountFirst() ) {
 325                     final int i = compareBySpeciesCount( domain_similarity );
 326                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 327                         return i;
 328                     }
 329                 }
 330                 if ( getMeanSimilarityScore() < domain_similarity.getMeanSimilarityScore() ) {
 331                     return PrintableDomainSimilarity.BEFORE;
 332                 }
 333                 else if ( getMeanSimilarityScore() > domain_similarity.getMeanSimilarityScore() ) {
 334                     return PrintableDomainSimilarity.AFTER;
 335                 }
 336                 else {
 337                     return compareByDomainId( domain_similarity );
 338                 }
 339             case SD:
 340                 if ( isSortBySpeciesCountFirst() ) {
 341                     final int i = compareBySpeciesCount( domain_similarity );
 342                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 343                         return i;
 344                     }
 345                 }
 346                 if ( getStandardDeviationOfSimilarityScore() < domain_similarity
 347                         .getStandardDeviationOfSimilarityScore() ) {
 348                     return PrintableDomainSimilarity.BEFORE;
 349                 }
 350                 else if ( getStandardDeviationOfSimilarityScore() > domain_similarity
 351                         .getStandardDeviationOfSimilarityScore() ) {
 352                     return PrintableDomainSimilarity.AFTER;
 353                 }
 354                 else {
 355                     return compareByDomainId( domain_similarity );
 356                 }
 357             case MAX_DIFFERENCE:
 358                 if ( isSortBySpeciesCountFirst() ) {
 359                     final int i = compareBySpeciesCount( domain_similarity );
 360                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 361                         return i;
 362                     }
 363                 }
 364                 if ( getMaximalDifference() > domain_similarity.getMaximalDifference() ) {
 365                     return PrintableDomainSimilarity.BEFORE;
 366                 }
 367                 else if ( getMaximalDifference() < domain_similarity.getMaximalDifference() ) {
 368                     return PrintableDomainSimilarity.AFTER;
 369                 }
 370                 else {
 371                     return compareByDomainId( domain_similarity );
 372                 }
 373             case ABS_MAX_COUNTS_DIFFERENCE:
 374                 if ( isSortBySpeciesCountFirst() ) {
 375                     final int i = compareBySpeciesCount( domain_similarity );
 376                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 377                         return i;
 378                     }
 379                 }
 380                 if ( Math.abs( getMaximalDifferenceInCounts() ) > Math.abs( domain_similarity
 381                         .getMaximalDifferenceInCounts() ) ) {
 382                     return PrintableDomainSimilarity.BEFORE;
 383                 }
 384                 else if ( Math.abs( getMaximalDifferenceInCounts() ) < Math.abs( domain_similarity
 385                         .getMaximalDifferenceInCounts() ) ) {
 386                     return PrintableDomainSimilarity.AFTER;
 387                 }
 388                 else {
 389                     return compareByDomainId( domain_similarity );
 390                 }
 391             case MAX_COUNTS_DIFFERENCE:
 392                 if ( getSpeciesData().size() != 2 ) {
 393                     throw new RuntimeException( "attempt to sort by maximal difference with species not equal to two" );
 394                 }
 395                 if ( isSortBySpeciesCountFirst() ) {
 396                     final int i = compareBySpeciesCount( domain_similarity );
 397                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 398                         return i;
 399                     }
 400                 }
 401                 if ( getMaximalDifferenceInCounts() > domain_similarity.getMaximalDifferenceInCounts() ) {
 402                     return PrintableDomainSimilarity.BEFORE;
 403                 }
 404                 else if ( getMaximalDifferenceInCounts() < domain_similarity.getMaximalDifferenceInCounts() ) {
 405                     return PrintableDomainSimilarity.AFTER;
 406                 }
 407                 else {
 408                     return compareByDomainId( domain_similarity );
 409                 }
 410             case SPECIES_COUNT:
 411                 final int i = compareBySpeciesCount( domain_similarity );
 412                 if ( i != PrintableDomainSimilarity.EQUAL ) {
 413                     return i;
 414                 }
 415                 else {
 416                     return compareByDomainId( domain_similarity );
 417                 }
 418             case DOMAIN_ID:
 419                 return compareByDomainId( domain_similarity );
 420         }
 421         throw new AssertionError( "Unknown sort method: " + getSortField() );
 422     }
 423
 424     @Override
 425     public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain ) {
 426         final SortedSet<DomainId> sorted_ids = new TreeSet<DomainId>();
 427         if ( getSpeciesData().containsKey( species_of_combinable_domain ) ) {
 428             for( final DomainId id : getSpeciesData().get( species_of_combinable_domain )
 429                     .getCombinableDomainIdToCountsMap().keySet() ) {
 430                 sorted_ids.add( id );
 431             }
 432         }
 433         return sorted_ids;
 434     }
 435
 436     private CombinableDomains getCombinableDomains() {
 437         return _combinable_domains;
 438     }
 439
 440     private DomainSimilarityCalculator.Detailedness getDetaildness() {
 441         return _detailedness;
 442     }
 443
 444     @Override
 445     public DomainId getDomainId() {
 446         return getCombinableDomains().getKeyDomain();
 447     }
 448
 449     private DomainSimilarityCalculator.GoAnnotationOutput getGoAnnotationOutput() {
 450         return _go_annotation_output;
 451     }
 452
 453     private Map<GoId, GoTerm> getGoIdToTermMap() {
 454         return _go_id_to_term_map;
 455     }
 456
 457     public GoNameSpace getGoNamespaceLimit() {
 458         return _go_namespace_limit;
 459     }
 460
 461     @Override
 462     public int getMaximalDifference() {
 463         return _max_difference;
 464     }
 465
 466     @Override
 467     public int getMaximalDifferenceInCounts() {
 468         return _max_difference_in_counts;
 469     }
 470
 471     @Override
 472     public double getMaximalSimilarityScore() {
 473         return _max;
 474     }
 475
 476     @Override
 477     public double getMeanSimilarityScore() {
 478         return _mean;
 479     }
 480
 481     @Override
 482     public double getMinimalSimilarityScore() {
 483         return _min;
 484     }
 485
 486     @Override
 487     public int getN() {
 488         return _n;
 489     }
 490
 491     private DomainSimilaritySortField getSortField() {
 492         return _sort_field;
 493     }
 494
 495     @Override
 496     public SortedSet<Species> getSpecies() {
 497         final SortedSet<Species> species = new TreeSet<Species>();
 498         for( final Species s : getSpeciesData().keySet() ) {
 499             species.add( s );
 500         }
 501         return species;
 502     }
 503
 504     public List<Species> getSpeciesCustomOrder() {
 505         return _species_order;
 506     }
 507
 508     @Override
 509     public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData() {
 510         return _species_data;
 511     }
 512
 513     private StringBuffer getSpeciesDataInAlphabeticalOrder( final boolean html ) {
 514         final StringBuffer sb = new StringBuffer();
 515         for( final Species species : getSpeciesData().keySet() ) {
 516             addSpeciesSpecificDomainData( sb, species, html );
 517         }
 518         return sb;
 519     }
 520
 521     private StringBuffer getSpeciesDataInCustomOrder( final boolean html ) {
 522         final StringBuffer sb = new StringBuffer();
 523         for( final Species order_species : getSpeciesCustomOrder() ) {
 524             if ( getSpeciesData().keySet().contains( order_species ) ) {
 525                 addSpeciesSpecificDomainData( sb, order_species, html );
 526             }
 527             else {
 528                 sb.append( PrintableDomainSimilarity.NO_SPECIES );
 529                 sb.append( PrintableDomainSimilarity.SPECIES_SEPARATOR );
 530             }
 531         }
 532         return sb;
 533     }
 534
 535     @Override
 536     public double getStandardDeviationOfSimilarityScore() {
 537         return _sd;
 538     }
 539
 540     private void init() {
 541         _detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 542         _go_annotation_output = null;
 543         _go_id_to_term_map = null;
 544     }
 545
 546     private boolean isSortBySpeciesCountFirst() {
 547         return _sort_by_species_count_first;
 548     }
 549
 550     private boolean isTreatAsBinaryComparison() {
 551         return _treat_as_binary_comparison;
 552     }
 553
 554     public void setDetailedness( final Detailedness detailedness ) {
 555         _detailedness = detailedness;
 556     }
 557
 558     public void setGoAnnotationOutput( final GoAnnotationOutput go_annotation_output ) {
 559         _go_annotation_output = go_annotation_output;
 560     }
 561
 562     public void setGoIdToTermMap( final Map<GoId, GoTerm> go_id_to_term_map ) {
 563         _go_id_to_term_map = go_id_to_term_map;
 564     }
 565
 566     public void setGoNamespaceLimit( final GoNameSpace go_namespace_limit ) {
 567         _go_namespace_limit = go_namespace_limit;
 568     }
 569
 570     public void setSpeciesOrder( final List<Species> species_order ) {
 571         if ( !species_order.containsAll( getSpeciesData().keySet() ) ) {
 572             throw new IllegalArgumentException( "list to order species must contain all species of multiple combinable domains similarity" );
 573         }
 574         _species_order = species_order;
 575     }
 576
 577     @Override
 578     public String toString() {
 579         return toStringBuffer( null ).toString();
 580     }
 581
 582     @Override
 583     public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option ) {
 584         switch ( print_option ) {
 585             case SIMPLE_TAB_DELIMITED:
 586                 return toStringBufferSimpleTabDelimited();
 587             case HTML:
 588                 return toStringBufferDetailedHTML();
 589             default:
 590                 throw new AssertionError( "Unknown print option: " + print_option );
 591         }
 592     }
 593
 594     private StringBuffer toStringBufferDetailedHTML() {
 595         final StringBuffer sb = new StringBuffer();
 596         sb.append( "<tr>" );
 597         sb.append( "<td>" );
 598         boldStartIfSortedBy( DomainSimilaritySortField.DOMAIN_ID, sb );
 599         sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + getDomainId() + "\">" + getDomainId()
 600                 + "</a>" );
 601         boldEndIfSortedBy( DomainSimilaritySortField.DOMAIN_ID, sb );
 602         sb.append( "</td>" );
 603         sb.append( "<td>" );
 604         boldStartIfSortedBy( DomainSimilaritySortField.MEAN, sb );
 605         sb.append( ForesterUtil.round( getMeanSimilarityScore(), 3 ) );
 606         boldEndIfSortedBy( DomainSimilaritySortField.MEAN, sb );
 607         sb.append( "</td>" );
 608         if ( !isTreatAsBinaryComparison() ) {
 609             sb.append( "<td>" );
 610             sb.append( "(" );
 611             boldStartIfSortedBy( DomainSimilaritySortField.SD, sb );
 612             sb.append( ForesterUtil.round( getStandardDeviationOfSimilarityScore(), 3 ) );
 613             boldEndIfSortedBy( DomainSimilaritySortField.SD, sb );
 614             sb.append( ")" );
 615             sb.append( "</td>" );
 616             sb.append( "<td>" );
 617             sb.append( "[" );
 618             boldStartIfSortedBy( DomainSimilaritySortField.MIN, sb );
 619             sb.append( ForesterUtil.round( getMinimalSimilarityScore(), 3 ) );
 620             boldEndIfSortedBy( DomainSimilaritySortField.MIN, sb );
 621             sb.append( "," );
 622             boldStartIfSortedBy( DomainSimilaritySortField.MAX, sb );
 623             sb.append( ForesterUtil.round( getMaximalSimilarityScore(), 3 ) );
 624             boldEndIfSortedBy( DomainSimilaritySortField.MAX, sb );
 625             sb.append( "]" );
 626             sb.append( "</td>" );
 627         }
 628         sb.append( "<td>" );
 629         boldStartIfSortedBy( DomainSimilaritySortField.MAX_DIFFERENCE, sb );
 630         sb.append( getMaximalDifference() );
 631         boldEndIfSortedBy( DomainSimilaritySortField.MAX_DIFFERENCE, sb );
 632         sb.append( "</td>" );
 633         sb.append( "<td>" );
 634         if ( isTreatAsBinaryComparison() ) {
 635             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 636             boldStartIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 637             sb.append( getMaximalDifferenceInCounts() );
 638             boldEndIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 639             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 640         }
 641         else {
 642             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 643             boldStartIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 644             sb.append( Math.abs( getMaximalDifferenceInCounts() ) );
 645             boldEndIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 646             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 647         }
 648         sb.append( "</td>" );
 649         if ( !isTreatAsBinaryComparison() ) {
 650             sb.append( "<td>" );
 651             if ( ( getSortField() == DomainSimilaritySortField.SPECIES_COUNT ) || isSortBySpeciesCountFirst() ) {
 652                 sb.append( "<b>" );
 653             }
 654             sb.append( getSpeciesData().size() );
 655             if ( ( getSortField() == DomainSimilaritySortField.SPECIES_COUNT ) || isSortBySpeciesCountFirst() ) {
 656                 sb.append( "</b>" );
 657             }
 658             sb.append( "</td>" );
 659         }
 660         if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
 661             sb.append( "<td>" );
 662             addGoInformation( sb, true, true );
 663             sb.append( "</td>" );
 664         }
 665         if ( ( getSpeciesCustomOrder() == null ) || getSpeciesCustomOrder().isEmpty() ) {
 666             sb.append( "<td>" );
 667             sb.append( getSpeciesDataInAlphabeticalOrder( true ) );
 668             sb.append( "</td>" );
 669         }
 670         else {
 671             sb.append( "<td>" );
 672             sb.append( getSpeciesDataInCustomOrder( true ) );
 673             sb.append( "</td>" );
 674         }
 675         sb.append( "</tr>" );
 676         return sb;
 677     }
 678
 679     private StringBuffer toStringBufferSimpleTabDelimited() {
 680         final StringBuffer sb = new StringBuffer();
 681         sb.append( getDomainId() );
 682         switch ( getSortField() ) {
 683             case MIN:
 684                 sb.append( TAB );
 685                 sb.append( ForesterUtil.round( getMinimalSimilarityScore(), 3 ) );
 686                 break;
 687             case MAX:
 688                 sb.append( TAB );
 689                 sb.append( ForesterUtil.round( getMaximalSimilarityScore(), 3 ) );
 690                 break;
 691             case MEAN:
 692                 sb.append( TAB );
 693                 sb.append( ForesterUtil.round( getMeanSimilarityScore(), 3 ) );
 694                 break;
 695             case SD:
 696                 sb.append( TAB );
 697                 sb.append( ForesterUtil.round( getStandardDeviationOfSimilarityScore(), 3 ) );
 698                 break;
 699             case MAX_DIFFERENCE:
 700                 sb.append( TAB );
 701                 sb.append( getMaximalDifference() );
 702             case ABS_MAX_COUNTS_DIFFERENCE:
 703             case MAX_COUNTS_DIFFERENCE:
 704                 sb.append( TAB );
 705                 if ( isTreatAsBinaryComparison() ) {
 706                     sb.append( getMaximalDifferenceInCounts() );
 707                 }
 708                 else {
 709                     sb.append( Math.abs( getMaximalDifferenceInCounts() ) );
 710                 }
 711                 break;
 712             case SPECIES_COUNT:
 713                 sb.append( TAB );
 714                 sb.append( getSpeciesData().size() );
 715                 break;
 716             case DOMAIN_ID:
 717                 break;
 718             default:
 719                 throw new AssertionError( "Unknown sort method: " + getSortField() );
 720         }
 721         if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
 722             sb.append( TAB );
 723             addGoInformation( sb, true, false );
 724         }
 725         return sb;
 726     }
 727
 728     public static enum PRINT_OPTION {
 729         SIMPLE_TAB_DELIMITED, HTML;
 730     }
 731 }