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.surfacing.DomainSimilarityCalculator.Detailedness;
  40 import org.forester.surfacing.DomainSimilarityCalculator.GoAnnotationOutput;
  41 import org.forester.util.ForesterUtil;
  42
  43 public class PrintableDomainSimilarity implements DomainSimilarity {
  44
  45     final public static String                                           SPECIES_SEPARATOR = "  ";
  46     final private static char                                            TAB               = '\t';
  47     final private static int                                             BEFORE            = -1;
  48     final private static int                                             EQUAL             = 0;
  49     final private static int                                             AFTER             = 1;
  50     final private static String                                          NO_SPECIES        = "     ";
  51     final private double                                                 _min;
  52     final private double                                                 _max;
  53     final private double                                                 _mean;
  54     final private double                                                 _sd;
  55     final private int                                                    _n;
  56     private final int                                                    _max_difference_in_counts;
  57     private final int                                                    _max_difference;
  58     private DomainSimilarityCalculator.GoAnnotationOutput                _go_annotation_output;
  59     final private CombinableDomains                                      _combinable_domains;
  60     final private SortedMap<Species, SpeciesSpecificDomainSimilariyData> _species_data;
  61     final private DomainSimilaritySortField                              _sort_field;
  62     private List<Species>                                                _species_order;
  63     private final boolean                                                _sort_by_species_count_first;
  64     private DomainSimilarityCalculator.Detailedness                      _detailedness;
  65     private Map<GoId, GoTerm>                                            _go_id_to_term_map;
  66     private GoNameSpace                                                  _go_namespace_limit;
  67     private final boolean                                                _treat_as_binary_comparison;
  68
  69     /**
  70      * If go_id_to_term_map not null, detailed GO information is written,
  71      * only GO ids otherwise.
  72      *
  73      *
  74      */
  75     public PrintableDomainSimilarity( final CombinableDomains combinable_domains,
  76                                       final double min,
  77                                       final double max,
  78                                       final double mean,
  79                                       final double median,
  80                                       final double sd,
  81                                       final int n,
  82                                       final int max_difference_in_counts,
  83                                       final int max_difference,
  84                                       final SortedMap<Species, SpeciesSpecificDomainSimilariyData> species_data,
  85                                       final DomainSimilaritySortField sort_field,
  86                                       final boolean sort_by_species_count_first,
  87                                       final boolean treat_as_binary_comparison ) {
  88         if ( combinable_domains == null ) {
  89             throw new IllegalArgumentException( "attempt to use null combinable domains" );
  90         }
  91         if ( sort_field == null ) {
  92             throw new IllegalArgumentException( "attempt to use null sorting" );
  93         }
  94         if ( species_data == null ) {
  95             throw new IllegalArgumentException( "attempt to use null species data" );
  96         }
  97         if ( species_data.size() < 1 ) {
  98             throw new IllegalArgumentException( "attempt to use empty species data" );
  99         }
 100         if ( n < 0 ) {
 101             throw new IllegalArgumentException( "attempt to use N less than 0" );
 102         }
 103         if ( ( species_data.size() > 1 ) && ( n < 1 ) ) {
 104             throw new IllegalArgumentException( "attempt to use N less than 1" );
 105         }
 106         if ( sd < 0.0 ) {
 107             throw new IllegalArgumentException( "attempt to use negative SD" );
 108         }
 109         if ( max < min ) {
 110             throw new IllegalArgumentException( "attempt to use max smaller than min" );
 111         }
 112         init();
 113         _combinable_domains = combinable_domains;
 114         _min = min;
 115         _max = max;
 116         _mean = mean;
 117         _sd = sd;
 118         _n = n;
 119         _max_difference_in_counts = max_difference_in_counts;
 120         _max_difference = max_difference;
 121         _species_data = species_data;
 122         _sort_field = sort_field;
 123         _sort_by_species_count_first = sort_by_species_count_first;
 124         _treat_as_binary_comparison = treat_as_binary_comparison;
 125         final int s = species_data.size();
 126         if ( ( ( s * s ) - s ) != ( getN() * 2 ) ) {
 127             throw new IllegalArgumentException( "illegal species count and n: species count:" + s + ", n:" + _n
 128                     + " for domain " + combinable_domains.getKeyDomain() );
 129         }
 130         if ( s > 2 ) {
 131             if ( getMaximalDifferenceInCounts() < 0 ) {
 132                 throw new IllegalArgumentException( "attempt to use negative max difference in counts with more than two species" );
 133             }
 134             if ( getMaximalDifference() < 0 ) {
 135                 throw new IllegalArgumentException( "attempt to use negative max difference with more than two species" );
 136             }
 137         }
 138     }
 139
 140     private void addGoInformation( final StringBuffer sb, final boolean for_table, final boolean html ) {
 141         if ( !for_table ) {
 142             sb.append( "<" );
 143         }
 144         switch ( getGoAnnotationOutput() ) {
 145             case ALL: {
 146                 final int go_ids = getCombinableDomains().getKeyDomain().getNumberOfGoIds();
 147                 boolean first = true;
 148                 for( int i = 0; i < go_ids; ++i ) {
 149                     final GoId go_id = getCombinableDomains().getKeyDomain().getGoId( i );
 150                     if ( getGoIdToTermMap() != null ) {
 151                         if ( getGoIdToTermMap().containsKey( go_id ) ) {
 152                             first = appendGoTerm( sb, getGoIdToTermMap().get( go_id ), first, html );
 153                         }
 154                         else {
 155                             sb.append( "go id \"" + go_id + "\" not found ["
 156                                     + getCombinableDomains().getKeyDomain().getId() + "]" );
 157                         }
 158                     }
 159                     else {
 160                         if ( !first ) {
 161                             sb.append( ", " );
 162                         }
 163                         if ( html ) {
 164                             sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id
 165                                     + "\" target=\"amigo_window\">" + go_id + "</a>" );
 166                         }
 167                         else {
 168                             sb.append( go_id );
 169                         }
 170                         first = false;
 171                     }
 172                 }
 173                 break;
 174             }
 175             case NONE: {
 176                 break;
 177             }
 178             default:
 179                 throw new RuntimeException( "unknown " + getGoAnnotationOutput() );
 180         }
 181         if ( !for_table ) {
 182             sb.append( ">: " );
 183         }
 184     }
 185
 186     private void addSpeciesSpecificDomainData( final StringBuffer sb, final Species species, final boolean html ) {
 187         if ( getDetaildness() != DomainSimilarityCalculator.Detailedness.BASIC ) {
 188             sb.append( "[" );
 189         }
 190         if ( html ) {
 191             sb.append( "<b>" );
 192             if ( ( SurfacingConstants.TAXONOMY_LINK != null ) && ( species.getSpeciesId().length() > 2 )
 193                     && ( species.getSpeciesId().length() < 6 ) ) {
 194                 sb.append( "<a href=\"" + SurfacingConstants.TAXONOMY_LINK + species.getSpeciesId()
 195                         + "\" target=\"taxonomy_window\">" + species.getSpeciesId() + "</a>" );
 196             }
 197             else {
 198                 sb.append( species.getSpeciesId() );
 199             }
 200             sb.append( "</b>" );
 201         }
 202         else {
 203             sb.append( species.getSpeciesId() );
 204         }
 205         if ( getDetaildness() != DomainSimilarityCalculator.Detailedness.BASIC ) {
 206             sb.append( ":" );
 207             sb.append( getSpeciesData().get( species ).toStringBuffer( getDetaildness(), html ) );
 208             sb.append( "]" );
 209         }
 210         if ( html ) {
 211             sb.append( "<br>" );
 212         }
 213         sb.append( PrintableDomainSimilarity.SPECIES_SEPARATOR );
 214     }
 215
 216     private boolean appendGoTerm( final StringBuffer sb, final GoTerm go_term, final boolean first, final boolean html ) {
 217         if ( ( getGoNamespaceLimit() == null ) || getGoNamespaceLimit().equals( go_term.getGoNameSpace() ) ) {
 218             if ( !first ) {
 219                 sb.append( ", " );
 220             }
 221             final GoId go_id = go_term.getGoId();
 222             if ( html ) {
 223                 sb.append( "<a href=\"" + SurfacingConstants.AMIGO_LINK + go_id + "\" target=\"amigo_window\">" + go_id
 224                         + "</a>" );
 225             }
 226             else {
 227                 sb.append( go_id );
 228             }
 229             sb.append( ":" );
 230             sb.append( go_term.getName() );
 231             if ( !html ) {
 232                 if ( getGoNamespaceLimit() == null ) {
 233                     sb.append( ":" );
 234                     sb.append( go_term.getGoNameSpace().toString() );
 235                 }
 236                 for( final GoXRef xref : go_term.getGoXRefs() ) {
 237                     sb.append( ":" );
 238                     sb.append( xref.toString() );
 239                 }
 240             }
 241             return false;
 242         }
 243         return true;
 244     }
 245
 246     private void boldEndIfSortedBy( final DomainSimilaritySortField sort_field, final StringBuffer sb ) {
 247         if ( getSortField() == sort_field ) {
 248             sb.append( "</b>" );
 249         }
 250     }
 251
 252     private void boldStartIfSortedBy( final DomainSimilaritySortField sort_field, final StringBuffer sb ) {
 253         if ( getSortField() == sort_field ) {
 254             sb.append( "<b>" );
 255         }
 256     }
 257
 258     private int compareByDomainId( final DomainSimilarity other ) {
 259         return getDomainId().compareTo( other.getDomainId() );
 260     }
 261
 262     private int compareBySpeciesCount( final DomainSimilarity domain_similarity ) {
 263         final int s_this = getSpeciesData().size();
 264         final int s_other = domain_similarity.getSpeciesData().size();
 265         if ( s_this < s_other ) {
 266             return PrintableDomainSimilarity.BEFORE;
 267         }
 268         else if ( s_this > s_other ) {
 269             return PrintableDomainSimilarity.AFTER;
 270         }
 271         else {
 272             return PrintableDomainSimilarity.EQUAL;
 273         }
 274     }
 275
 276     public int compareTo( final DomainSimilarity domain_similarity ) {
 277         if ( this == domain_similarity ) {
 278             return PrintableDomainSimilarity.EQUAL;
 279         }
 280         else if ( domain_similarity == null ) {
 281             throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to null" );
 282         }
 283         else if ( domain_similarity.getClass() != this.getClass() ) {
 284             throw new IllegalArgumentException( "attempt to compare " + this.getClass() + " to "
 285                     + domain_similarity.getClass() );
 286         }
 287         switch ( getSortField() ) {
 288             case MIN:
 289                 if ( isSortBySpeciesCountFirst() ) {
 290                     final int i = compareBySpeciesCount( domain_similarity );
 291                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 292                         return i;
 293                     }
 294                 }
 295                 if ( getMinimalSimilarityScore() < domain_similarity.getMinimalSimilarityScore() ) {
 296                     return PrintableDomainSimilarity.BEFORE;
 297                 }
 298                 else if ( getMinimalSimilarityScore() > domain_similarity.getMinimalSimilarityScore() ) {
 299                     return PrintableDomainSimilarity.AFTER;
 300                 }
 301                 else {
 302                     return compareByDomainId( domain_similarity );
 303                 }
 304             case MAX:
 305                 if ( isSortBySpeciesCountFirst() ) {
 306                     final int i = compareBySpeciesCount( domain_similarity );
 307                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 308                         return i;
 309                     }
 310                 }
 311                 if ( getMaximalSimilarityScore() < domain_similarity.getMaximalSimilarityScore() ) {
 312                     return PrintableDomainSimilarity.BEFORE;
 313                 }
 314                 else if ( getMaximalSimilarityScore() > domain_similarity.getMaximalSimilarityScore() ) {
 315                     return PrintableDomainSimilarity.AFTER;
 316                 }
 317                 else {
 318                     return compareByDomainId( domain_similarity );
 319                 }
 320             case MEAN:
 321                 if ( isSortBySpeciesCountFirst() ) {
 322                     final int i = compareBySpeciesCount( domain_similarity );
 323                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 324                         return i;
 325                     }
 326                 }
 327                 if ( getMeanSimilarityScore() < domain_similarity.getMeanSimilarityScore() ) {
 328                     return PrintableDomainSimilarity.BEFORE;
 329                 }
 330                 else if ( getMeanSimilarityScore() > domain_similarity.getMeanSimilarityScore() ) {
 331                     return PrintableDomainSimilarity.AFTER;
 332                 }
 333                 else {
 334                     return compareByDomainId( domain_similarity );
 335                 }
 336             case SD:
 337                 if ( isSortBySpeciesCountFirst() ) {
 338                     final int i = compareBySpeciesCount( domain_similarity );
 339                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 340                         return i;
 341                     }
 342                 }
 343                 if ( getStandardDeviationOfSimilarityScore() < domain_similarity
 344                         .getStandardDeviationOfSimilarityScore() ) {
 345                     return PrintableDomainSimilarity.BEFORE;
 346                 }
 347                 else if ( getStandardDeviationOfSimilarityScore() > domain_similarity
 348                         .getStandardDeviationOfSimilarityScore() ) {
 349                     return PrintableDomainSimilarity.AFTER;
 350                 }
 351                 else {
 352                     return compareByDomainId( domain_similarity );
 353                 }
 354             case MAX_DIFFERENCE:
 355                 if ( isSortBySpeciesCountFirst() ) {
 356                     final int i = compareBySpeciesCount( domain_similarity );
 357                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 358                         return i;
 359                     }
 360                 }
 361                 if ( getMaximalDifference() > domain_similarity.getMaximalDifference() ) {
 362                     return PrintableDomainSimilarity.BEFORE;
 363                 }
 364                 else if ( getMaximalDifference() < domain_similarity.getMaximalDifference() ) {
 365                     return PrintableDomainSimilarity.AFTER;
 366                 }
 367                 else {
 368                     return compareByDomainId( domain_similarity );
 369                 }
 370             case ABS_MAX_COUNTS_DIFFERENCE:
 371                 if ( isSortBySpeciesCountFirst() ) {
 372                     final int i = compareBySpeciesCount( domain_similarity );
 373                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 374                         return i;
 375                     }
 376                 }
 377                 if ( Math.abs( getMaximalDifferenceInCounts() ) > Math.abs( domain_similarity
 378                         .getMaximalDifferenceInCounts() ) ) {
 379                     return PrintableDomainSimilarity.BEFORE;
 380                 }
 381                 else if ( Math.abs( getMaximalDifferenceInCounts() ) < Math.abs( domain_similarity
 382                         .getMaximalDifferenceInCounts() ) ) {
 383                     return PrintableDomainSimilarity.AFTER;
 384                 }
 385                 else {
 386                     return compareByDomainId( domain_similarity );
 387                 }
 388             case MAX_COUNTS_DIFFERENCE:
 389                 if ( getSpeciesData().size() != 2 ) {
 390                     throw new RuntimeException( "attempt to sort by maximal difference with species not equal to two" );
 391                 }
 392                 if ( isSortBySpeciesCountFirst() ) {
 393                     final int i = compareBySpeciesCount( domain_similarity );
 394                     if ( i != PrintableDomainSimilarity.EQUAL ) {
 395                         return i;
 396                     }
 397                 }
 398                 if ( getMaximalDifferenceInCounts() > domain_similarity.getMaximalDifferenceInCounts() ) {
 399                     return PrintableDomainSimilarity.BEFORE;
 400                 }
 401                 else if ( getMaximalDifferenceInCounts() < domain_similarity.getMaximalDifferenceInCounts() ) {
 402                     return PrintableDomainSimilarity.AFTER;
 403                 }
 404                 else {
 405                     return compareByDomainId( domain_similarity );
 406                 }
 407             case SPECIES_COUNT:
 408                 final int i = compareBySpeciesCount( domain_similarity );
 409                 if ( i != PrintableDomainSimilarity.EQUAL ) {
 410                     return i;
 411                 }
 412                 else {
 413                     return compareByDomainId( domain_similarity );
 414                 }
 415             case DOMAIN_ID:
 416                 return compareByDomainId( domain_similarity );
 417         }
 418         throw new AssertionError( "Unknown sort method: " + getSortField() );
 419     }
 420
 421     public SortedSet<DomainId> getCombinableDomainIds( final Species species_of_combinable_domain ) {
 422         final SortedSet<DomainId> sorted_ids = new TreeSet<DomainId>();
 423         if ( getSpeciesData().containsKey( species_of_combinable_domain ) ) {
 424             for( final DomainId id : getSpeciesData().get( species_of_combinable_domain )
 425                     .getCombinableDomainIdToCountsMap().keySet() ) {
 426                 sorted_ids.add( id );
 427             }
 428         }
 429         return sorted_ids;
 430     }
 431
 432     private CombinableDomains getCombinableDomains() {
 433         return _combinable_domains;
 434     }
 435
 436     private DomainSimilarityCalculator.Detailedness getDetaildness() {
 437         return _detailedness;
 438     }
 439
 440     public DomainId getDomainId() {
 441         return getCombinableDomains().getKeyDomain();
 442     }
 443
 444     private DomainSimilarityCalculator.GoAnnotationOutput getGoAnnotationOutput() {
 445         return _go_annotation_output;
 446     }
 447
 448     private Map<GoId, GoTerm> getGoIdToTermMap() {
 449         return _go_id_to_term_map;
 450     }
 451
 452     public GoNameSpace getGoNamespaceLimit() {
 453         return _go_namespace_limit;
 454     }
 455
 456     public int getMaximalDifference() {
 457         return _max_difference;
 458     }
 459
 460     @Override
 461     public int getMaximalDifferenceInCounts() {
 462         return _max_difference_in_counts;
 463     }
 464
 465     public double getMaximalSimilarityScore() {
 466         return _max;
 467     }
 468
 469     public double getMeanSimilarityScore() {
 470         return _mean;
 471     }
 472
 473     public double getMinimalSimilarityScore() {
 474         return _min;
 475     }
 476
 477     public int getN() {
 478         return _n;
 479     }
 480
 481     private DomainSimilaritySortField getSortField() {
 482         return _sort_field;
 483     }
 484
 485     public SortedSet<Species> getSpecies() {
 486         final SortedSet<Species> species = new TreeSet<Species>();
 487         for( final Species s : getSpeciesData().keySet() ) {
 488             species.add( s );
 489         }
 490         return species;
 491     }
 492
 493     public List<Species> getSpeciesCustomOrder() {
 494         return _species_order;
 495     }
 496
 497     public SortedMap<Species, SpeciesSpecificDomainSimilariyData> getSpeciesData() {
 498         return _species_data;
 499     }
 500
 501     private StringBuffer getSpeciesDataInAlphabeticalOrder( final boolean html ) {
 502         final StringBuffer sb = new StringBuffer();
 503         for( final Species species : getSpeciesData().keySet() ) {
 504             addSpeciesSpecificDomainData( sb, species, html );
 505         }
 506         return sb;
 507     }
 508
 509     private StringBuffer getSpeciesDataInCustomOrder( final boolean html ) {
 510         final StringBuffer sb = new StringBuffer();
 511         for( final Species order_species : getSpeciesCustomOrder() ) {
 512             if ( getSpeciesData().keySet().contains( order_species ) ) {
 513                 addSpeciesSpecificDomainData( sb, order_species, html );
 514             }
 515             else {
 516                 sb.append( PrintableDomainSimilarity.NO_SPECIES );
 517                 sb.append( PrintableDomainSimilarity.SPECIES_SEPARATOR );
 518             }
 519         }
 520         return sb;
 521     }
 522
 523     public double getStandardDeviationOfSimilarityScore() {
 524         return _sd;
 525     }
 526
 527     private void init() {
 528         _detailedness = DomainSimilarityCalculator.Detailedness.PUNCTILIOUS;
 529         _go_annotation_output = null;
 530         _go_id_to_term_map = null;
 531     }
 532
 533     private boolean isSortBySpeciesCountFirst() {
 534         return _sort_by_species_count_first;
 535     }
 536
 537     private boolean isTreatAsBinaryComparison() {
 538         return _treat_as_binary_comparison;
 539     }
 540
 541     public void setDetailedness( final Detailedness detailedness ) {
 542         _detailedness = detailedness;
 543     }
 544
 545     public void setGoAnnotationOutput( final GoAnnotationOutput go_annotation_output ) {
 546         _go_annotation_output = go_annotation_output;
 547     }
 548
 549     public void setGoIdToTermMap( final Map<GoId, GoTerm> go_id_to_term_map ) {
 550         _go_id_to_term_map = go_id_to_term_map;
 551     }
 552
 553     public void setGoNamespaceLimit( final GoNameSpace go_namespace_limit ) {
 554         _go_namespace_limit = go_namespace_limit;
 555     }
 556
 557     public void setSpeciesOrder( final List<Species> species_order ) {
 558         if ( !species_order.containsAll( getSpeciesData().keySet() ) ) {
 559             throw new IllegalArgumentException( "list to order species must contain all species of multiple combinable domains similarity" );
 560         }
 561         _species_order = species_order;
 562     }
 563
 564     @Override
 565     public String toString() {
 566         return toStringBuffer( null ).toString();
 567     }
 568
 569     public StringBuffer toStringBuffer( final PrintableDomainSimilarity.PRINT_OPTION print_option ) {
 570         switch ( print_option ) {
 571             case SIMPLE_TAB_DELIMITED:
 572                 return toStringBufferSimpleTabDelimited();
 573             case HTML:
 574                 return toStringBufferDetailedHTML();
 575             default:
 576                 throw new AssertionError( "Unknown print option: " + print_option );
 577         }
 578     }
 579
 580     private StringBuffer toStringBufferDetailedHTML() {
 581         final StringBuffer sb = new StringBuffer();
 582         sb.append( "<tr>" );
 583         sb.append( "<td>" );
 584         boldStartIfSortedBy( DomainSimilaritySortField.DOMAIN_ID, sb );
 585         sb.append( "<a href=\"" + SurfacingConstants.PFAM_FAMILY_ID_LINK + getDomainId() + "\">" + getDomainId()
 586                 + "</a>" );
 587         boldEndIfSortedBy( DomainSimilaritySortField.DOMAIN_ID, sb );
 588         sb.append( "</td>" );
 589         sb.append( "<td>" );
 590         boldStartIfSortedBy( DomainSimilaritySortField.MEAN, sb );
 591         sb.append( ForesterUtil.round( getMeanSimilarityScore(), 3 ) );
 592         boldEndIfSortedBy( DomainSimilaritySortField.MEAN, sb );
 593         sb.append( "</td>" );
 594         if ( !isTreatAsBinaryComparison() ) {
 595             sb.append( "<td>" );
 596             sb.append( "(" );
 597             boldStartIfSortedBy( DomainSimilaritySortField.SD, sb );
 598             sb.append( ForesterUtil.round( getStandardDeviationOfSimilarityScore(), 3 ) );
 599             boldEndIfSortedBy( DomainSimilaritySortField.SD, sb );
 600             sb.append( ")" );
 601             sb.append( "</td>" );
 602             sb.append( "<td>" );
 603             sb.append( "[" );
 604             boldStartIfSortedBy( DomainSimilaritySortField.MIN, sb );
 605             sb.append( ForesterUtil.round( getMinimalSimilarityScore(), 3 ) );
 606             boldEndIfSortedBy( DomainSimilaritySortField.MIN, sb );
 607             sb.append( "," );
 608             boldStartIfSortedBy( DomainSimilaritySortField.MAX, sb );
 609             sb.append( ForesterUtil.round( getMaximalSimilarityScore(), 3 ) );
 610             boldEndIfSortedBy( DomainSimilaritySortField.MAX, sb );
 611             sb.append( "]" );
 612             sb.append( "</td>" );
 613         }
 614         sb.append( "<td>" );
 615         boldStartIfSortedBy( DomainSimilaritySortField.MAX_DIFFERENCE, sb );
 616         sb.append( getMaximalDifference() );
 617         boldEndIfSortedBy( DomainSimilaritySortField.MAX_DIFFERENCE, sb );
 618         sb.append( "</td>" );
 619         sb.append( "<td>" );
 620         if ( isTreatAsBinaryComparison() ) {
 621             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 622             boldStartIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 623             sb.append( getMaximalDifferenceInCounts() );
 624             boldEndIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 625             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 626         }
 627         else {
 628             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 629             boldStartIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 630             sb.append( Math.abs( getMaximalDifferenceInCounts() ) );
 631             boldEndIfSortedBy( DomainSimilaritySortField.ABS_MAX_COUNTS_DIFFERENCE, sb );
 632             boldStartIfSortedBy( DomainSimilaritySortField.MAX_COUNTS_DIFFERENCE, sb );
 633         }
 634         sb.append( "</td>" );
 635         if ( !isTreatAsBinaryComparison() ) {
 636             sb.append( "<td>" );
 637             if ( ( getSortField() == DomainSimilaritySortField.SPECIES_COUNT ) || isSortBySpeciesCountFirst() ) {
 638                 sb.append( "<b>" );
 639             }
 640             sb.append( getSpeciesData().size() );
 641             if ( ( getSortField() == DomainSimilaritySortField.SPECIES_COUNT ) || isSortBySpeciesCountFirst() ) {
 642                 sb.append( "</b>" );
 643             }
 644             sb.append( "</td>" );
 645         }
 646         if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
 647             sb.append( "<td>" );
 648             addGoInformation( sb, true, true );
 649             sb.append( "</td>" );
 650         }
 651         if ( ( getSpeciesCustomOrder() == null ) || getSpeciesCustomOrder().isEmpty() ) {
 652             sb.append( "<td>" );
 653             sb.append( getSpeciesDataInAlphabeticalOrder( true ) );
 654             sb.append( "</td>" );
 655         }
 656         else {
 657             sb.append( "<td>" );
 658             sb.append( getSpeciesDataInCustomOrder( true ) );
 659             sb.append( "</td>" );
 660         }
 661         sb.append( "</tr>" );
 662         return sb;
 663     }
 664
 665     private StringBuffer toStringBufferSimpleTabDelimited() {
 666         final StringBuffer sb = new StringBuffer();
 667         sb.append( getDomainId() );
 668         switch ( getSortField() ) {
 669             case MIN:
 670                 sb.append( TAB );
 671                 sb.append( ForesterUtil.round( getMinimalSimilarityScore(), 3 ) );
 672                 break;
 673             case MAX:
 674                 sb.append( TAB );
 675                 sb.append( ForesterUtil.round( getMaximalSimilarityScore(), 3 ) );
 676                 break;
 677             case MEAN:
 678                 sb.append( TAB );
 679                 sb.append( ForesterUtil.round( getMeanSimilarityScore(), 3 ) );
 680                 break;
 681             case SD:
 682                 sb.append( TAB );
 683                 sb.append( ForesterUtil.round( getStandardDeviationOfSimilarityScore(), 3 ) );
 684                 break;
 685             case MAX_DIFFERENCE:
 686                 sb.append( TAB );
 687                 sb.append( getMaximalDifference() );
 688             case ABS_MAX_COUNTS_DIFFERENCE:
 689             case MAX_COUNTS_DIFFERENCE:
 690                 sb.append( TAB );
 691                 if ( isTreatAsBinaryComparison() ) {
 692                     sb.append( getMaximalDifferenceInCounts() );
 693                 }
 694                 else {
 695                     sb.append( Math.abs( getMaximalDifferenceInCounts() ) );
 696                 }
 697                 break;
 698             case SPECIES_COUNT:
 699                 sb.append( TAB );
 700                 sb.append( getSpeciesData().size() );
 701                 break;
 702             case DOMAIN_ID:
 703                 break;
 704             default:
 705                 throw new AssertionError( "Unknown sort method: " + getSortField() );
 706         }
 707         if ( getGoAnnotationOutput() != DomainSimilarityCalculator.GoAnnotationOutput.NONE ) {
 708             sb.append( TAB );
 709             addGoInformation( sb, true, false );
 710         }
 711         return sb;
 712     }
 713
 714     public static enum PRINT_OPTION {
 715         SIMPLE_TAB_DELIMITED, HTML;
 716     }
 717 }