forester/java/src/org/forester/io/parsers/HmmscanPerDomainTableParser.java

   1 // $Id:
   2 // $
   3 //
   4 // FORESTER -- software libraries and applications
   5 // for evolutionary biology research and applications.
   6 //
   7 // Copyright (C) 2008-2009 Christian M. Zmasek
   8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
   9 // All rights reserved
  10 //
  11 // This library is free software; you can redistribute it and/or
  12 // modify it under the terms of the GNU Lesser General Public
  13 // License as published by the Free Software Foundation; either
  14 // version 2.1 of the License, or (at your option) any later version.
  15 //
  16 // This library is distributed in the hope that it will be useful,
  17 // but WITHOUT ANY WARRANTY; without even the implied warranty of
  18 // MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
  19 // Lesser General Public License for more details.
  20 //
  21 // You should have received a copy of the GNU Lesser General Public
  22 // License along with this library; if not, write to the Free Software
  23 // Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
  24 //
  25 // Contact: phylosoft @ gmail . com
  26 // WWW: www.phylosoft.org/forester
  27
  28 package org.forester.io.parsers;
  29
  30 import java.io.BufferedReader;
  31 import java.io.File;
  32 import java.io.FileReader;
  33 import java.io.IOException;
  34 import java.util.ArrayList;
  35 import java.util.Date;
  36 import java.util.HashSet;
  37 import java.util.List;
  38 import java.util.Map;
  39 import java.util.Set;
  40 import java.util.SortedSet;
  41 import java.util.TreeMap;
  42 import java.util.TreeSet;
  43
  44 import org.forester.surfacing.BasicDomain;
  45 import org.forester.surfacing.BasicProtein;
  46 import org.forester.surfacing.Domain;
  47 import org.forester.surfacing.DomainId;
  48 import org.forester.surfacing.Protein;
  49 import org.forester.surfacing.SurfacingUtil;
  50 import org.forester.util.ForesterUtil;
  51
  52 public final class HmmscanPerDomainTableParser {
  53
  54     private static final String           RETRO                       = "RETRO";
  55     private static final String           PHAGE                       = "PHAGE";
  56     private static final String           VIR                         = "VIR";
  57     private static final String           TRANSPOS                    = "TRANSPOS";
  58     private static final String           RV                          = "RV";
  59     private static final String           GAG                         = "GAG_";
  60     private static final String           HCV                         = "HCV_";
  61     private static final String           HERPES                      = "HERPES_";
  62     private static final String           BACULO                      = "BACULO_";
  63     private static final int              E_VALUE_MAXIMUM_DEFAULT     = -1;
  64     private static final ReturnType       RETURN_TYPE_DEFAULT         = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
  65     private static final boolean          IGNORE_DUFS_DEFAULT         = false;
  66     private static final int              MAX_ALLOWED_OVERLAP_DEFAULT = -1;
  67     private final Set<DomainId>           _filter;
  68     private final FilterType              _filter_type;
  69     private final File                    _input_file;
  70     private final String                  _species;
  71     private double                        _e_value_maximum;
  72     private Map<String, Double>           _individual_score_cutoffs;
  73     private boolean                       _ignore_dufs;
  74     private boolean                       _ignore_virus_like_ids;
  75     private int                           _max_allowed_overlap;
  76     private boolean                       _ignore_engulfed_domains;
  77     private ReturnType                    _return_type;
  78     private int                           _proteins_encountered;
  79     private int                           _proteins_ignored_due_to_filter;
  80     private int                           _proteins_stored;
  81     private int                           _domains_encountered;
  82     private int                           _domains_ignored_due_to_duf;
  83     private int                           _domains_ignored_due_to_overlap;
  84     private int                           _domains_ignored_due_to_e_value;
  85     private int                           _domains_ignored_due_to_individual_score_cutoff;
  86     private int                           _domains_stored;
  87     private SortedSet<DomainId>           _domains_stored_set;
  88     private long                          _time;
  89     private int                           _domains_ignored_due_to_negative_domain_filter;
  90     private Map<String, Integer>          _domains_ignored_due_to_negative_domain_filter_counts_map;
  91     private int                           _domains_ignored_due_to_virus_like_id;
  92     private Map<String, Integer>          _domains_ignored_due_to_virus_like_id_counts_map;
  93     private final INDIVIDUAL_SCORE_CUTOFF _ind_cutoff;
  94
  95     public HmmscanPerDomainTableParser( final File input_file,
  96                                         final String species,
  97                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
  98         _input_file = input_file;
  99         _species = species;
 100         _filter = null;
 101         _filter_type = FilterType.NONE;
 102         _ind_cutoff = individual_cutoff_applies_to;
 103         init();
 104     }
 105
 106     public HmmscanPerDomainTableParser( final File input_file,
 107                                         final String species,
 108                                         final Set<DomainId> filter,
 109                                         final FilterType filter_type,
 110                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
 111         _input_file = input_file;
 112         _species = species;
 113         _filter = filter;
 114         _filter_type = filter_type;
 115         _ind_cutoff = individual_cutoff_applies_to;
 116         init();
 117     }
 118
 119     private void actuallyAddProtein( final List<Protein> proteins, final Protein current_protein ) {
 120         final List<Domain> l = current_protein.getProteinDomains();
 121         for( final Domain d : l ) {
 122             getDomainsStoredSet().add( d.getDomainId() );
 123         }
 124         proteins.add( current_protein );
 125         ++_proteins_stored;
 126     }
 127
 128     private void addProtein( final List<Protein> proteins, Protein current_protein ) {
 129         if ( ( getMaxAllowedOverlap() != HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT )
 130                 || isIgnoreEngulfedDomains() ) {
 131             final int domains_count = current_protein.getNumberOfProteinDomains();
 132             current_protein = SurfacingUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
 133                                                                       isIgnoreEngulfedDomains(),
 134                                                                       current_protein );
 135             final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
 136             _domains_stored -= domains_removed;
 137             _domains_ignored_due_to_overlap += domains_removed;
 138         }
 139         if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
 140             final Set<DomainId> domain_ids_in_protein = new HashSet<DomainId>();
 141             for( final Domain d : current_protein.getProteinDomains() ) {
 142                 domain_ids_in_protein.add( d.getDomainId() );
 143             }
 144             domain_ids_in_protein.retainAll( getFilter() );
 145             if ( getFilterType() == FilterType.POSITIVE_PROTEIN ) {
 146                 if ( domain_ids_in_protein.size() > 0 ) {
 147                     actuallyAddProtein( proteins, current_protein );
 148                 }
 149                 else {
 150                     ++_proteins_ignored_due_to_filter;
 151                 }
 152             }
 153             else {
 154                 if ( domain_ids_in_protein.size() < 1 ) {
 155                     actuallyAddProtein( proteins, current_protein );
 156                 }
 157                 else {
 158                     ++_proteins_ignored_due_to_filter;
 159                 }
 160             }
 161         }
 162         else {
 163             actuallyAddProtein( proteins, current_protein );
 164         }
 165     }
 166
 167     public int getDomainsEncountered() {
 168         return _domains_encountered;
 169     }
 170
 171     public int getDomainsIgnoredDueToDuf() {
 172         return _domains_ignored_due_to_duf;
 173     }
 174
 175     public int getDomainsIgnoredDueToEval() {
 176         return _domains_ignored_due_to_e_value;
 177     }
 178
 179     public int getDomainsIgnoredDueToIndividualScoreCutoff() {
 180         return _domains_ignored_due_to_individual_score_cutoff;
 181     }
 182
 183     public int getDomainsIgnoredDueToNegativeDomainFilter() {
 184         return _domains_ignored_due_to_negative_domain_filter;
 185     }
 186
 187     public Map<String, Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap() {
 188         return _domains_ignored_due_to_negative_domain_filter_counts_map;
 189     }
 190
 191     public int getDomainsIgnoredDueToOverlap() {
 192         return _domains_ignored_due_to_overlap;
 193     }
 194
 195     public Map<String, Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap() {
 196         return _domains_ignored_due_to_virus_like_id_counts_map;
 197     }
 198
 199     public int getDomainsIgnoredDueToVirusLikeIds() {
 200         return _domains_ignored_due_to_virus_like_id;
 201     }
 202
 203     public int getDomainsStored() {
 204         return _domains_stored;
 205     }
 206
 207     public SortedSet<DomainId> getDomainsStoredSet() {
 208         return _domains_stored_set;
 209     }
 210
 211     private double getEValueMaximum() {
 212         return _e_value_maximum;
 213     }
 214
 215     private Set<DomainId> getFilter() {
 216         return _filter;
 217     }
 218
 219     private FilterType getFilterType() {
 220         return _filter_type;
 221     }
 222
 223     public INDIVIDUAL_SCORE_CUTOFF getIndividualCutoffAppliesTo() {
 224         return _ind_cutoff;
 225     }
 226
 227     private Map<String, Double> getIndividualScoreCutoffs() {
 228         return _individual_score_cutoffs;
 229     }
 230
 231     private File getInputFile() {
 232         return _input_file;
 233     }
 234
 235     private int getMaxAllowedOverlap() {
 236         return _max_allowed_overlap;
 237     }
 238
 239     public int getProteinsEncountered() {
 240         return _proteins_encountered;
 241     }
 242
 243     public int getProteinsIgnoredDueToFilter() {
 244         return _proteins_ignored_due_to_filter;
 245     }
 246
 247     public int getProteinsStored() {
 248         return _proteins_stored;
 249     }
 250
 251     private ReturnType getReturnType() {
 252         return _return_type;
 253     }
 254
 255     private String getSpecies() {
 256         return _species;
 257     }
 258
 259     public long getTime() {
 260         return _time;
 261     }
 262
 263     private void init() {
 264         _e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT;
 265         setIgnoreDufs( HmmscanPerDomainTableParser.IGNORE_DUFS_DEFAULT );
 266         setReturnType( HmmscanPerDomainTableParser.RETURN_TYPE_DEFAULT );
 267         _max_allowed_overlap = HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT;
 268         setIndividualScoreCutoffs( null );
 269         setIgnoreEngulfedDomains( false );
 270         setIgnoreVirusLikeIds( false );
 271         intitCounts();
 272     }
 273
 274     private void intitCounts() {
 275         setDomainsStoredSet( new TreeSet<DomainId>() );
 276         setDomainsEncountered( 0 );
 277         setProteinsEncountered( 0 );
 278         setProteinsIgnoredDueToFilter( 0 );
 279         setDomainsIgnoredDueToNegativeFilter( 0 );
 280         setDomainsIgnoredDueToDuf( 0 );
 281         setDomainsIgnoredDueToEval( 0 );
 282         setDomainsIgnoredDueToIndividualScoreCutoff( 0 );
 283         setDomainsIgnoredDueToVirusLikeId( 0 );
 284         setDomainsIgnoredDueToOverlap( 0 );
 285         setDomainsStored( 0 );
 286         setProteinsStored( 0 );
 287         setTime( 0 );
 288         setDomainsIgnoredDueToVirusLikeIdCountsMap( new TreeMap<String, Integer>() );
 289         setDomainsIgnoredDueToNegativeDomainFilterCountsMap( new TreeMap<String, Integer>() );
 290     }
 291
 292     private boolean isIgnoreDufs() {
 293         return _ignore_dufs;
 294     }
 295
 296     private boolean isIgnoreEngulfedDomains() {
 297         return _ignore_engulfed_domains;
 298     }
 299
 300     private boolean isIgnoreVirusLikeIds() {
 301         return _ignore_virus_like_ids;
 302     }
 303
 304     public List<Protein> parse() throws IOException {
 305         if ( ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.NONE )
 306                 && ( ( getIndividualScoreCutoffs() == null ) || ( getIndividualScoreCutoffs().size() < 1 ) ) ) {
 307             throw new RuntimeException( "attempt to use individual cuttoffs with having set them" );
 308         }
 309         intitCounts();
 310         final Set<String> prev_queries = new HashSet<String>();
 311         final String error = ForesterUtil.isReadableFile( getInputFile() );
 312         if ( !ForesterUtil.isEmpty( error ) ) {
 313             throw new IOException( error );
 314         }
 315         final BufferedReader br = new BufferedReader( new FileReader( getInputFile() ) );
 316         String line;
 317         final List<Protein> proteins = new ArrayList<Protein>();
 318         Protein current_protein = null;
 319         int line_number = 0;
 320         final long start_time = new Date().getTime();
 321         String prev_query = "";
 322         int prev_qlen = -1;
 323         while ( ( line = br.readLine() ) != null ) {
 324             line_number++;
 325             if ( ForesterUtil.isEmpty( line ) || line.startsWith( "#" ) ) {
 326                 continue;
 327             }
 328             // 0                    1           2    3                      4           5      6        7      8      9  10  11        12        13     14    15      16  17      18  19      20  21  22
 329             // #                                                                              --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
 330             // # target name        accession   tlen query name             accession   qlen   E-value  score  bias   #  of  c-Evalue  i-Evalue  score  bias  from    to  from    to  from    to  acc description of target
 331             // #------------------- ---------- -----   -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
 332             // Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   1   4   1.5e-41     3e-38  130.8  11.1     3   171   140   307   139   346 0.81 Ion transport protein
 333             // Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   2   4   9.1e-45   1.8e-41  141.3  13.1     4   200   479   664   476   665 0.97 Ion transport protein
 334             // Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   3   4   5.2e-45     1e-41  142.1  14.0     1   201   900  1117   900  1117 0.96 Ion transport protein
 335             // Ion_trans            PF00520.24   201 jgi|Nemve1|7|gw.28.1.1 -           1604  6.3e-169  557.4  95.3   4   4   9.2e-51   1.8e-47  160.9  11.3     1   201  1217  1423  1217  1423 0.97 Ion transport protein
 336             // PKD_channel          PF08016.5    426 jgi|Nemve1|7|gw.28.1.1 -           1604   5.9e-19   67.4  70.5   1   8   0.00053       1.1    7.3   0.4   220   264   142   191   134   200 0.73 Polycystin cation channel
 337             final String tokens[] = line.split( "\\s+" );
 338             final String target_id = tokens[ 0 ];
 339             final String target_acc = tokens[ 1 ];
 340             final int tlen = parseInt( tokens[ 2 ], line_number, "tlen" );
 341             final String query = tokens[ 3 ];
 342             final String query_acc = tokens[ 4 ];
 343             final int qlen = parseInt( tokens[ 5 ], line_number, "qlen" );
 344             final double fs_e_value = parseDouble( tokens[ 6 ], line_number, "E-value" );
 345             final double fs_score = parseDouble( tokens[ 7 ], line_number, "score" );
 346             final int domain_number = parseInt( tokens[ 9 ], line_number, "count" );
 347             final int total_domains = parseInt( tokens[ 10 ], line_number, "total" );
 348             final double c_e_value = parseDouble( tokens[ 11 ], line_number, "c-Evalue" );
 349             final double i_e_value = parseDouble( tokens[ 12 ], line_number, "i-Evalue" );
 350             final double domain_score = parseDouble( tokens[ 13 ], line_number, "score" );
 351             final int hmm_from = parseInt( tokens[ 15 ], line_number, "hmm from" );
 352             final int hmm_to = parseInt( tokens[ 16 ], line_number, "hmm to" );
 353             final int ali_from = parseInt( tokens[ 17 ], line_number, "ali from" );
 354             final int ali_to = parseInt( tokens[ 18 ], line_number, "ali to" );
 355             final int env_from = parseInt( tokens[ 19 ], line_number, "env from" );
 356             final int env_to = parseInt( tokens[ 20 ], line_number, "env to" );
 357             ++_domains_encountered;
 358             if ( !query.equals( prev_query ) || ( qlen != prev_qlen ) ) {
 359                 if ( query.equals( prev_query ) ) {
 360                     throw new IOException( "more than one protein named [" + query + "]" + " lengths: " + qlen + ", "
 361                             + prev_qlen );
 362                 }
 363                 if ( prev_queries.contains( query ) ) {
 364                     throw new IOException( "more than one protein named [" + query + "]" );
 365                 }
 366                 prev_query = query;
 367                 prev_qlen = qlen;
 368                 prev_queries.add( query );
 369                 if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
 370                     addProtein( proteins, current_protein );
 371                 }
 372                 if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
 373                     current_protein = new BasicProtein( query, getSpecies() );
 374                 }
 375                 else {
 376                     throw new IllegalArgumentException( "unknown return type" );
 377                 }
 378             }
 379             boolean failed_cutoff = false;
 380             if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.NONE ) {
 381                 if ( getIndividualScoreCutoffs().containsKey( target_id ) ) {
 382                     final double cutoff = getIndividualScoreCutoffs().get( target_id );
 383                     if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE ) {
 384                         if ( fs_score < cutoff ) {
 385                             failed_cutoff = true;
 386                         }
 387                     }
 388                     else if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.DOMAIN ) {
 389                         if ( domain_score < cutoff ) {
 390                             failed_cutoff = true;
 391                         }
 392                     }
 393                 }
 394                 else {
 395                     throw new IOException( "could not find a score cutoff value for domain id \"" + target_id
 396                             + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
 397                 }
 398             }
 399             final String uc_id = target_id.toUpperCase();
 400             if ( failed_cutoff ) {
 401                 ++_domains_ignored_due_to_individual_score_cutoff;
 402             }
 403             else if ( ali_from == ali_to ) {
 404                 //Ignore
 405             }
 406             else if ( ( getEValueMaximum() != HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT )
 407                     && ( fs_e_value > getEValueMaximum() ) ) {
 408                 ++_domains_ignored_due_to_e_value;
 409             }
 410             else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) {
 411                 ++_domains_ignored_due_to_duf;
 412             }
 413             else if ( isIgnoreVirusLikeIds()
 414                     && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
 415                             || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )
 416                             || uc_id.startsWith( HCV ) || uc_id.startsWith( HERPES ) || uc_id.startsWith( BACULO ) ) ) {
 417                 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), target_id );
 418                 ++_domains_ignored_due_to_virus_like_id;
 419             }
 420             else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN )
 421                     && getFilter().contains( new DomainId( target_id ) ) ) {
 422                 ++_domains_ignored_due_to_negative_domain_filter;
 423                 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), target_id );
 424             }
 425             else {
 426                 try {
 427                     final Domain pd = new BasicDomain( target_id,
 428                                                        ali_from,
 429                                                        ali_to,
 430                                                        ( short ) domain_number,
 431                                                        ( short ) total_domains,
 432                                                        fs_e_value,
 433                                                        fs_score,
 434                                                        i_e_value,
 435                                                        domain_score );
 436                     current_protein.addProteinDomain( pd );
 437                 }
 438                 catch ( final IllegalArgumentException e ) {
 439                     throw new IOException( "problem with domain parsing at line " + line_number + "[" + line + "]: "
 440                             + e.getMessage() );
 441                 }
 442                 ++_domains_stored;
 443             }
 444         } // while ( ( line = br.readLine() ) != null )
 445         if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
 446             addProtein( proteins, current_protein );
 447         }
 448         setProteinsEncountered( prev_queries.size() );
 449         setTime( new Date().getTime() - start_time );
 450         return proteins;
 451     }
 452
 453     private double parseDouble( final String double_str, final int line_number, final String label ) throws IOException {
 454         double d = -1;
 455         try {
 456             d = Double.valueOf( double_str ).doubleValue();
 457         }
 458         catch ( final NumberFormatException e ) {
 459             throw new IOException( "could not parse \" +label + \" from \"" + double_str + "\" [line " + line_number
 460                     + "] in [" + getInputFile().getCanonicalPath() + "]" );
 461         }
 462         return d;
 463     }
 464
 465     private int parseInt( final String double_str, final int line_number, final String label ) throws IOException {
 466         int i = -1;
 467         try {
 468             i = Integer.valueOf( double_str ).intValue();
 469         }
 470         catch ( final NumberFormatException e ) {
 471             throw new IOException( "could not parse \"" + label + "\" from \"" + double_str + "\" [line " + line_number
 472                     + "] in [" + getInputFile().getCanonicalPath() + "]" );
 473         }
 474         return i;
 475     }
 476
 477     private void setDomainsEncountered( final int domains_encountered ) {
 478         _domains_encountered = domains_encountered;
 479     }
 480
 481     private void setDomainsIgnoredDueToDuf( final int domains_ignored_due_to_duf ) {
 482         _domains_ignored_due_to_duf = domains_ignored_due_to_duf;
 483     }
 484
 485     private void setDomainsIgnoredDueToEval( final int domains_ignored_due_to_e_value ) {
 486         _domains_ignored_due_to_e_value = domains_ignored_due_to_e_value;
 487     }
 488
 489     private void setDomainsIgnoredDueToIndividualScoreCutoff( final int domains_ignored_due_to_individual_score_cutoff ) {
 490         _domains_ignored_due_to_individual_score_cutoff = domains_ignored_due_to_individual_score_cutoff;
 491     }
 492
 493     private void setDomainsIgnoredDueToNegativeDomainFilterCountsMap( final Map<String, Integer> domains_ignored_due_to_negative_domain_filter_counts_map ) {
 494         _domains_ignored_due_to_negative_domain_filter_counts_map = domains_ignored_due_to_negative_domain_filter_counts_map;
 495     }
 496
 497     private void setDomainsIgnoredDueToNegativeFilter( final int domains_ignored_due_to_negative_domain_filter ) {
 498         _domains_ignored_due_to_negative_domain_filter = domains_ignored_due_to_negative_domain_filter;
 499     }
 500
 501     private void setDomainsIgnoredDueToOverlap( final int domains_ignored_due_to_overlap ) {
 502         _domains_ignored_due_to_overlap = domains_ignored_due_to_overlap;
 503     }
 504
 505     private void setDomainsIgnoredDueToVirusLikeId( final int i ) {
 506         _domains_ignored_due_to_virus_like_id = i;
 507     }
 508
 509     private void setDomainsIgnoredDueToVirusLikeIdCountsMap( final Map<String, Integer> domains_ignored_due_to_virus_like_id_counts_map ) {
 510         _domains_ignored_due_to_virus_like_id_counts_map = domains_ignored_due_to_virus_like_id_counts_map;
 511     }
 512
 513     private void setDomainsStored( final int domains_stored ) {
 514         _domains_stored = domains_stored;
 515     }
 516
 517     private void setDomainsStoredSet( final SortedSet<DomainId> _storeddomains_stored ) {
 518         _domains_stored_set = _storeddomains_stored;
 519     }
 520
 521     public void setEValueMaximum( final double e_value_maximum ) {
 522         if ( e_value_maximum < 0.0 ) {
 523             throw new IllegalArgumentException( "attempt to set the maximum E-value to a negative value" );
 524         }
 525         _e_value_maximum = e_value_maximum;
 526     }
 527
 528     public void setIgnoreDufs( final boolean ignore_dufs ) {
 529         _ignore_dufs = ignore_dufs;
 530     }
 531
 532     /**
 533      * To ignore domains which are completely engulfed by domains (individual
 534      * ones or stretches of overlapping ones) with better support values.
 535      *
 536      *
 537      * @param ignored_engulfed_domains
 538      */
 539     public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) {
 540         _ignore_engulfed_domains = ignore_engulfed_domains;
 541     }
 542
 543     public void setIgnoreVirusLikeIds( final boolean ignore_virus_like_ids ) {
 544         _ignore_virus_like_ids = ignore_virus_like_ids;
 545     }
 546
 547     /**
 548      * Sets the individual  score cutoff values (for example, gathering
 549      * thresholds from Pfam). Domain ids are the keys, cutoffs the values.
 550      *
 551      * @param individual_score_cutoffs
 552      */
 553     public void setIndividualScoreCutoffs( final Map<String, Double> individual_score_cutoffs ) {
 554         _individual_score_cutoffs = individual_score_cutoffs;
 555     }
 556
 557     public void setMaxAllowedOverlap( final int max_allowed_overlap ) {
 558         if ( max_allowed_overlap < 0 ) {
 559             throw new IllegalArgumentException( "Attempt to set max allowed overlap to less than zero." );
 560         }
 561         _max_allowed_overlap = max_allowed_overlap;
 562     }
 563
 564     private void setProteinsEncountered( final int proteins_encountered ) {
 565         _proteins_encountered = proteins_encountered;
 566     }
 567
 568     private void setProteinsIgnoredDueToFilter( final int proteins_ignored_due_to_filter ) {
 569         _proteins_ignored_due_to_filter = proteins_ignored_due_to_filter;
 570     }
 571
 572     private void setProteinsStored( final int proteins_stored ) {
 573         _proteins_stored = proteins_stored;
 574     }
 575
 576     public void setReturnType( final ReturnType return_type ) {
 577         _return_type = return_type;
 578     }
 579
 580     private void setTime( final long time ) {
 581         _time = time;
 582     }
 583
 584     public static enum FilterType {
 585         NONE, POSITIVE_PROTEIN, NEGATIVE_PROTEIN, NEGATIVE_DOMAIN
 586     }
 587
 588     static public enum INDIVIDUAL_SCORE_CUTOFF {
 589         FULL_SEQUENCE, DOMAIN, NONE;
 590     }
 591
 592     public static enum ReturnType {
 593         UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN
 594     }
 595 }