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