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: https://sites.google.com/site/cmzmasek/home/software/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.protein.BasicDomain;
  45 import org.forester.protein.BasicProtein;
  46 import org.forester.protein.Domain;
  47 import org.forester.protein.Protein;
  48 import org.forester.util.ForesterUtil;
  49
  50 public final class HmmscanPerDomainTableParser {
  51
  52     private static final String           RETRO                       = "RETRO";
  53     private static final String           PHAGE                       = "PHAGE";
  54     private static final String           VIR                         = "VIR";
  55     private static final String           TRANSPOS                    = "TRANSPOS";
  56     private static final String           RV                          = "RV";
  57     private static final String           GAG                         = "GAG_";
  58     private static final String           HCV                         = "HCV_";
  59     private static final String           HERPES                      = "HERPES_";
  60     private static final String           BACULO                      = "BACULO_";
  61     private static final int              E_VALUE_MAXIMUM_DEFAULT     = -1;
  62     private static final ReturnType       RETURN_TYPE_DEFAULT         = ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN;
  63     private static final boolean          IGNORE_DUFS_DEFAULT         = false;
  64     private static final int              MAX_ALLOWED_OVERLAP_DEFAULT = -1;
  65     private static final boolean          IGNORE_REPLACED_RRMS        = false;
  66     private static final boolean          IGNORE_hGDE_amylase         = true;                                                      //TODO eventually remove me, added 10/22/13
  67     private final Set<String>             _filter;
  68     private final FilterType              _filter_type;
  69     private final File                    _input_file;
  70     private final String                  _species;
  71     private double                        _fs_e_value_maximum;
  72     private double                        _i_e_value_maximum;
  73     private Map<String, Double>           _individual_score_cutoffs;
  74     private boolean                       _ignore_dufs;
  75     private boolean                       _ignore_virus_like_ids;
  76     private int                           _max_allowed_overlap;
  77     private boolean                       _ignore_engulfed_domains;
  78     private ReturnType                    _return_type;
  79     private int                           _proteins_encountered;
  80     private int                           _proteins_ignored_due_to_filter;
  81     private int                           _proteins_stored;
  82     private int                           _domains_encountered;
  83     private int                           _domains_ignored_due_to_duf;
  84     private int                           _domains_ignored_due_to_overlap;
  85     private int                           _domains_ignored_due_to_fs_e_value;
  86     private int                           _domains_ignored_due_to_i_e_value;
  87     private int                           _domains_ignored_due_to_individual_score_cutoff;
  88     private int                           _domains_stored;
  89     private SortedSet<String>             _domains_stored_set;
  90     private long                          _time;
  91     private int                           _domains_ignored_due_to_negative_domain_filter;
  92     private Map<String, Integer>          _domains_ignored_due_to_negative_domain_filter_counts_map;
  93     private int                           _domains_ignored_due_to_virus_like_id;
  94     private Map<String, Integer>          _domains_ignored_due_to_virus_like_id_counts_map;
  95     private final INDIVIDUAL_SCORE_CUTOFF _ind_cutoff;
  96     private final boolean                 _allow_proteins_with_same_name;
  97
  98     public HmmscanPerDomainTableParser( final File input_file,
  99                                         final String species,
 100                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
 101         _input_file = input_file;
 102         _species = species;
 103         _filter = null;
 104         _filter_type = FilterType.NONE;
 105         _ind_cutoff = individual_cutoff_applies_to;
 106         _allow_proteins_with_same_name = false;
 107         init();
 108     }
 109
 110     public HmmscanPerDomainTableParser( final File input_file,
 111                                         final String species,
 112                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
 113                                         final boolean allow_proteins_with_same_name ) {
 114         _input_file = input_file;
 115         _species = species;
 116         _filter = null;
 117         _filter_type = FilterType.NONE;
 118         _ind_cutoff = individual_cutoff_applies_to;
 119         _allow_proteins_with_same_name = allow_proteins_with_same_name;
 120         init();
 121     }
 122
 123     public HmmscanPerDomainTableParser( final File input_file,
 124                                         final String species,
 125                                         final Set<String> filter,
 126                                         final FilterType filter_type,
 127                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
 128         _input_file = input_file;
 129         _species = species;
 130         _filter = filter;
 131         _filter_type = filter_type;
 132         _ind_cutoff = individual_cutoff_applies_to;
 133         _allow_proteins_with_same_name = false;
 134         init();
 135     }
 136
 137     public HmmscanPerDomainTableParser( final File input_file,
 138                                         final String species,
 139                                         final Set<String> filter,
 140                                         final FilterType filter_type,
 141                                         final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
 142                                         final boolean allow_proteins_with_same_name ) {
 143         _input_file = input_file;
 144         _species = species;
 145         _filter = filter;
 146         _filter_type = filter_type;
 147         _ind_cutoff = individual_cutoff_applies_to;
 148         _allow_proteins_with_same_name = allow_proteins_with_same_name;
 149         init();
 150     }
 151
 152     public boolean isAllowProteinsWithSameName() {
 153         return _allow_proteins_with_same_name;
 154     }
 155
 156     private void actuallyAddProtein( final List<Protein> proteins, final Protein current_protein ) {
 157         final List<Domain> l = current_protein.getProteinDomains();
 158         for( final Domain d : l ) {
 159             getDomainsStoredSet().add( d.getDomainId() );
 160         }
 161         proteins.add( current_protein );
 162         ++_proteins_stored;
 163     }
 164
 165     private void addProtein( final List<Protein> proteins, Protein current_protein ) {
 166         if ( ( getMaxAllowedOverlap() != HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT )
 167                 || isIgnoreEngulfedDomains() ) {
 168             final int domains_count = current_protein.getNumberOfProteinDomains();
 169             current_protein = ForesterUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
 170                                                                      isIgnoreEngulfedDomains(),
 171                                                                      current_protein );
 172             final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
 173             _domains_stored -= domains_removed;
 174             _domains_ignored_due_to_overlap += domains_removed;
 175         }
 176         if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
 177             final Set<String> domain_ids_in_protein = new HashSet<String>();
 178             for( final Domain d : current_protein.getProteinDomains() ) {
 179                 domain_ids_in_protein.add( d.getDomainId() );
 180             }
 181             domain_ids_in_protein.retainAll( getFilter() );
 182             if ( getFilterType() == FilterType.POSITIVE_PROTEIN ) {
 183                 if ( domain_ids_in_protein.size() > 0 ) {
 184                     actuallyAddProtein( proteins, current_protein );
 185                 }
 186                 else {
 187                     ++_proteins_ignored_due_to_filter;
 188                 }
 189             }
 190             else {
 191                 if ( domain_ids_in_protein.size() < 1 ) {
 192                     actuallyAddProtein( proteins, current_protein );
 193                 }
 194                 else {
 195                     ++_proteins_ignored_due_to_filter;
 196                 }
 197             }
 198         }
 199         else {
 200             actuallyAddProtein( proteins, current_protein );
 201         }
 202     }
 203
 204     public int getDomainsEncountered() {
 205         return _domains_encountered;
 206     }
 207
 208     public int getDomainsIgnoredDueToDuf() {
 209         return _domains_ignored_due_to_duf;
 210     }
 211
 212     public int getDomainsIgnoredDueToIEval() {
 213         return _domains_ignored_due_to_i_e_value;
 214     }
 215
 216     public int getDomainsIgnoredDueToFsEval() {
 217         return _domains_ignored_due_to_fs_e_value;
 218     }
 219
 220     public int getDomainsIgnoredDueToIndividualScoreCutoff() {
 221         return _domains_ignored_due_to_individual_score_cutoff;
 222     }
 223
 224     public int getDomainsIgnoredDueToNegativeDomainFilter() {
 225         return _domains_ignored_due_to_negative_domain_filter;
 226     }
 227
 228     public Map<String, Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap() {
 229         return _domains_ignored_due_to_negative_domain_filter_counts_map;
 230     }
 231
 232     public int getDomainsIgnoredDueToOverlap() {
 233         return _domains_ignored_due_to_overlap;
 234     }
 235
 236     public Map<String, Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap() {
 237         return _domains_ignored_due_to_virus_like_id_counts_map;
 238     }
 239
 240     public int getDomainsIgnoredDueToVirusLikeIds() {
 241         return _domains_ignored_due_to_virus_like_id;
 242     }
 243
 244     public int getDomainsStored() {
 245         return _domains_stored;
 246     }
 247
 248     public SortedSet<String> getDomainsStoredSet() {
 249         return _domains_stored_set;
 250     }
 251
 252     private double getFsEValueMaximum() {
 253         return _fs_e_value_maximum;
 254     }
 255
 256     private double getIEValueMaximum() {
 257         return _i_e_value_maximum;
 258     }
 259
 260     private Set<String> getFilter() {
 261         return _filter;
 262     }
 263
 264     private FilterType getFilterType() {
 265         return _filter_type;
 266     }
 267
 268     public INDIVIDUAL_SCORE_CUTOFF getIndividualCutoffAppliesTo() {
 269         return _ind_cutoff;
 270     }
 271
 272     private Map<String, Double> getIndividualScoreCutoffs() {
 273         return _individual_score_cutoffs;
 274     }
 275
 276     private File getInputFile() {
 277         return _input_file;
 278     }
 279
 280     private int getMaxAllowedOverlap() {
 281         return _max_allowed_overlap;
 282     }
 283
 284     public int getProteinsEncountered() {
 285         return _proteins_encountered;
 286     }
 287
 288     public int getProteinsIgnoredDueToFilter() {
 289         return _proteins_ignored_due_to_filter;
 290     }
 291
 292     public int getProteinsStored() {
 293         return _proteins_stored;
 294     }
 295
 296     private ReturnType getReturnType() {
 297         return _return_type;
 298     }
 299
 300     private String getSpecies() {
 301         return _species;
 302     }
 303
 304     public long getTime() {
 305         return _time;
 306     }
 307
 308     private void init() {
 309         _fs_e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT;
 310         _i_e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT;
 311         setIgnoreDufs( HmmscanPerDomainTableParser.IGNORE_DUFS_DEFAULT );
 312         setReturnType( HmmscanPerDomainTableParser.RETURN_TYPE_DEFAULT );
 313         _max_allowed_overlap = HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT;
 314         setIndividualScoreCutoffs( null );
 315         setIgnoreEngulfedDomains( false );
 316         setIgnoreVirusLikeIds( false );
 317         intitCounts();
 318     }
 319
 320     private void intitCounts() {
 321         setDomainsStoredSet( new TreeSet<String>() );
 322         setDomainsEncountered( 0 );
 323         setProteinsEncountered( 0 );
 324         setProteinsIgnoredDueToFilter( 0 );
 325         setDomainsIgnoredDueToNegativeFilter( 0 );
 326         setDomainsIgnoredDueToDuf( 0 );
 327         setDomainsIgnoredDueToFsEval( 0 );
 328         setDomainsIgnoredDueToIEval( 0 );
 329         setDomainsIgnoredDueToIndividualScoreCutoff( 0 );
 330         setDomainsIgnoredDueToVirusLikeId( 0 );
 331         setDomainsIgnoredDueToOverlap( 0 );
 332         setDomainsStored( 0 );
 333         setProteinsStored( 0 );
 334         setTime( 0 );
 335         setDomainsIgnoredDueToVirusLikeIdCountsMap( new TreeMap<String, Integer>() );
 336         setDomainsIgnoredDueToNegativeDomainFilterCountsMap( new TreeMap<String, Integer>() );
 337     }
 338
 339     private boolean isIgnoreDufs() {
 340         return _ignore_dufs;
 341     }
 342
 343     private boolean isIgnoreEngulfedDomains() {
 344         return _ignore_engulfed_domains;
 345     }
 346
 347     private boolean isIgnoreVirusLikeIds() {
 348         return _ignore_virus_like_ids;
 349     }
 350
 351     public List<Protein> parse() throws IOException {
 352         if ( ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.NONE )
 353                 && ( ( getIndividualScoreCutoffs() == null ) || ( getIndividualScoreCutoffs().size() < 1 ) ) ) {
 354             throw new RuntimeException( "attempt to use individual cuttoffs with having set them" );
 355         }
 356         intitCounts();
 357         final Set<String> prev_queries = new HashSet<String>();
 358         final String error = ForesterUtil.isReadableFile( getInputFile() );
 359         if ( !ForesterUtil.isEmpty( error ) ) {
 360             throw new IOException( error );
 361         }
 362         final BufferedReader br = new BufferedReader( new FileReader( getInputFile() ) );
 363         String line;
 364         final List<Protein> proteins = new ArrayList<Protein>();
 365         Protein current_protein = null;
 366         int line_number = 0;
 367         final long start_time = new Date().getTime();
 368         String prev_query = "";
 369         int prev_qlen = -1;
 370         while ( ( line = br.readLine() ) != null ) {
 371             line_number++;
 372             if ( ForesterUtil.isEmpty( line ) || line.startsWith( "#" ) ) {
 373                 continue;
 374             }
 375             // 0                    1           2    3                      4           5      6        7      8      9  10  11        12        13     14    15      16  17      18  19      20  21  22
 376             // #                                                                              --- full sequence --- -------------- this domain -------------   hmm coord   ali coord   env coord
 377             // # 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
 378             // #------------------- ---------- -----   -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
 379             // 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
 380             // 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
 381             // 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
 382             // 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
 383             // 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
 384             final String tokens[] = line.split( "\\s+" );
 385             final String target_id = tokens[ 0 ];
 386             final String target_acc = tokens[ 1 ];
 387             final int tlen = parseInt( tokens[ 2 ], line_number, "tlen" );
 388             final String query = tokens[ 3 ];
 389             final String query_acc = tokens[ 4 ];
 390             final int qlen = parseInt( tokens[ 5 ], line_number, "qlen" );
 391             final double fs_e_value = parseDouble( tokens[ 6 ], line_number, "E-value" );
 392             final double fs_score = parseDouble( tokens[ 7 ], line_number, "score" );
 393             final int domain_number = parseInt( tokens[ 9 ], line_number, "count" );
 394             final int total_domains = parseInt( tokens[ 10 ], line_number, "total" );
 395             final double c_e_value = parseDouble( tokens[ 11 ], line_number, "c-Evalue" );
 396             final double i_e_value = parseDouble( tokens[ 12 ], line_number, "i-Evalue" );
 397             final double domain_score = parseDouble( tokens[ 13 ], line_number, "score" );
 398             final int hmm_from = parseInt( tokens[ 15 ], line_number, "hmm from" );
 399             final int hmm_to = parseInt( tokens[ 16 ], line_number, "hmm to" );
 400             final int ali_from = parseInt( tokens[ 17 ], line_number, "ali from" );
 401             final int ali_to = parseInt( tokens[ 18 ], line_number, "ali to" );
 402             final int env_from = parseInt( tokens[ 19 ], line_number, "env from" );
 403             final int env_to = parseInt( tokens[ 20 ], line_number, "env to" );
 404             ++_domains_encountered;
 405             if ( !query.equals( prev_query ) || ( qlen != prev_qlen ) ) {
 406                 if ( !isAllowProteinsWithSameName() ) {
 407                     if ( query.equals( prev_query ) ) {
 408                         throw new IOException( "more than one protein named [" + query + "]" + " lengths: " + qlen
 409                                                + ", " + prev_qlen );
 410                     }
 411                     if ( prev_queries.contains( query ) ) {
 412                         throw new IOException( "more than one protein named [" + query + "]" );
 413                     }
 414                 }
 415                 prev_query = query;
 416                 prev_qlen = qlen;
 417                 prev_queries.add( query );
 418                 if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
 419                     addProtein( proteins, current_protein );
 420                 }
 421                 if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
 422                     current_protein = new BasicProtein( query, getSpecies(), qlen );
 423                 }
 424                 else {
 425                     throw new IllegalArgumentException( "unknown return type" );
 426                 }
 427             }
 428             boolean failed_cutoff = false;
 429             if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.NONE ) {
 430                 if ( getIndividualScoreCutoffs().containsKey( target_id ) ) {
 431                     final double cutoff = getIndividualScoreCutoffs().get( target_id );
 432                     if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE ) {
 433                         if ( fs_score < cutoff ) {
 434                             failed_cutoff = true;
 435                         }
 436                     }
 437                     else if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.DOMAIN ) {
 438                         if ( domain_score < cutoff ) {
 439                             failed_cutoff = true;
 440                         }
 441                     }
 442                 }
 443                 else {
 444                     throw new IOException( "could not find a score cutoff value for domain id \"" + target_id
 445                                            + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
 446                 }
 447             }
 448             final String uc_id = target_id.toUpperCase();
 449             if ( failed_cutoff ) {
 450                 ++_domains_ignored_due_to_individual_score_cutoff;
 451             }
 452             else if ( ali_from == ali_to ) {
 453                 //Ignore
 454             }
 455             else if ( ( getFsEValueMaximum() != HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT )
 456                     && ( fs_e_value > getFsEValueMaximum() ) ) {
 457                 ++_domains_ignored_due_to_fs_e_value;
 458             }
 459             else if ( ( getIEValueMaximum() != HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT )
 460                     && ( i_e_value > getIEValueMaximum() ) ) {
 461                 ++_domains_ignored_due_to_i_e_value;
 462             }
 463             else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) {
 464                 ++_domains_ignored_due_to_duf;
 465             }
 466             else if ( IGNORE_REPLACED_RRMS
 467                     && ( uc_id.contains( "RRM_1" ) || uc_id.contains( "RRM_3" ) || uc_id.contains( "RRM_5" ) || uc_id
 468                             .contains( "RRM_6" ) ) ) {
 469             }
 470             else if ( IGNORE_hGDE_amylase && ( uc_id.equals( "hGDE_amylase" ) ) ) {
 471             }
 472             else if ( isIgnoreVirusLikeIds()
 473                     && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
 474                             || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )
 475                             || uc_id.startsWith( HCV ) || uc_id.startsWith( HERPES ) || uc_id.startsWith( BACULO ) ) ) {
 476                 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), target_id );
 477                 ++_domains_ignored_due_to_virus_like_id;
 478             }
 479             else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN ) && getFilter().contains( target_id ) ) {
 480                 ++_domains_ignored_due_to_negative_domain_filter;
 481                 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), target_id );
 482             }
 483             else {
 484                 try {
 485                     final Domain pd = new BasicDomain( target_id,
 486                                                        ali_from,
 487                                                        ali_to,
 488                                                        ( short ) domain_number,
 489                                                        ( short ) total_domains,
 490                                                        i_e_value,
 491                                                        domain_score );
 492                     current_protein.addProteinDomain( pd );
 493                 }
 494                 catch ( final IllegalArgumentException e ) {
 495                     throw new IOException( "problem with domain parsing at line " + line_number + "[" + line + "]: "
 496                             + e.getMessage() );
 497                 }
 498                 ++_domains_stored;
 499             }
 500         } // while ( ( line = br.readLine() ) != null )
 501         if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
 502             addProtein( proteins, current_protein );
 503         }
 504         setProteinsEncountered( prev_queries.size() );
 505         setTime( new Date().getTime() - start_time );
 506         return proteins;
 507     }
 508
 509     private double parseDouble( final String double_str, final int line_number, final String label ) throws IOException {
 510         double d = -1;
 511         try {
 512             d = Double.valueOf( double_str ).doubleValue();
 513         }
 514         catch ( final NumberFormatException e ) {
 515             throw new IOException( "could not parse \" +label + \" from \"" + double_str + "\" [line " + line_number
 516                                    + "] in [" + getInputFile().getCanonicalPath() + "]" );
 517         }
 518         return d;
 519     }
 520
 521     private int parseInt( final String double_str, final int line_number, final String label ) throws IOException {
 522         int i = -1;
 523         try {
 524             i = Integer.valueOf( double_str ).intValue();
 525         }
 526         catch ( final NumberFormatException e ) {
 527             throw new IOException( "could not parse \"" + label + "\" from \"" + double_str + "\" [line " + line_number
 528                                    + "] in [" + getInputFile().getCanonicalPath() + "]" );
 529         }
 530         return i;
 531     }
 532
 533     private void setDomainsEncountered( final int domains_encountered ) {
 534         _domains_encountered = domains_encountered;
 535     }
 536
 537     private void setDomainsIgnoredDueToDuf( final int domains_ignored_due_to_duf ) {
 538         _domains_ignored_due_to_duf = domains_ignored_due_to_duf;
 539     }
 540
 541     private void setDomainsIgnoredDueToFsEval( final int domains_ignored_due_to_fs_e_value ) {
 542         _domains_ignored_due_to_fs_e_value = domains_ignored_due_to_fs_e_value;
 543     }
 544
 545     private void setDomainsIgnoredDueToIEval( final int domains_ignored_due_to_i_e_value ) {
 546         _domains_ignored_due_to_i_e_value = domains_ignored_due_to_i_e_value;
 547     }
 548
 549     private void setDomainsIgnoredDueToIndividualScoreCutoff( final int domains_ignored_due_to_individual_score_cutoff ) {
 550         _domains_ignored_due_to_individual_score_cutoff = domains_ignored_due_to_individual_score_cutoff;
 551     }
 552
 553     private void setDomainsIgnoredDueToNegativeDomainFilterCountsMap( final Map<String, Integer> domains_ignored_due_to_negative_domain_filter_counts_map ) {
 554         _domains_ignored_due_to_negative_domain_filter_counts_map = domains_ignored_due_to_negative_domain_filter_counts_map;
 555     }
 556
 557     private void setDomainsIgnoredDueToNegativeFilter( final int domains_ignored_due_to_negative_domain_filter ) {
 558         _domains_ignored_due_to_negative_domain_filter = domains_ignored_due_to_negative_domain_filter;
 559     }
 560
 561     private void setDomainsIgnoredDueToOverlap( final int domains_ignored_due_to_overlap ) {
 562         _domains_ignored_due_to_overlap = domains_ignored_due_to_overlap;
 563     }
 564
 565     private void setDomainsIgnoredDueToVirusLikeId( final int i ) {
 566         _domains_ignored_due_to_virus_like_id = i;
 567     }
 568
 569     private void setDomainsIgnoredDueToVirusLikeIdCountsMap( final Map<String, Integer> domains_ignored_due_to_virus_like_id_counts_map ) {
 570         _domains_ignored_due_to_virus_like_id_counts_map = domains_ignored_due_to_virus_like_id_counts_map;
 571     }
 572
 573     private void setDomainsStored( final int domains_stored ) {
 574         _domains_stored = domains_stored;
 575     }
 576
 577     private void setDomainsStoredSet( final SortedSet<String> _storeddomains_stored ) {
 578         _domains_stored_set = _storeddomains_stored;
 579     }
 580
 581     public void setFsEValueMaximum( final double fs_e_value_maximum ) {
 582         if ( fs_e_value_maximum < 0.0 ) {
 583             throw new IllegalArgumentException( "attempt to set the maximum E-value to a negative value" );
 584         }
 585         _fs_e_value_maximum = fs_e_value_maximum;
 586     }
 587
 588     public void setIEValueMaximum( final double i_e_value_maximum ) {
 589         if ( i_e_value_maximum < 0.0 ) {
 590             throw new IllegalArgumentException( "attempt to set the maximum E-value to a negative value" );
 591         }
 592         _i_e_value_maximum = i_e_value_maximum;
 593     }
 594
 595     public void setIgnoreDufs( final boolean ignore_dufs ) {
 596         _ignore_dufs = ignore_dufs;
 597     }
 598
 599     /**
 600      * To ignore domains which are completely engulfed by domains (individual
 601      * ones or stretches of overlapping ones) with better support values.
 602      *
 603      *
 604      * @param ignored_engulfed_domains
 605      */
 606     public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) {
 607         _ignore_engulfed_domains = ignore_engulfed_domains;
 608     }
 609
 610     public void setIgnoreVirusLikeIds( final boolean ignore_virus_like_ids ) {
 611         _ignore_virus_like_ids = ignore_virus_like_ids;
 612     }
 613
 614     /**
 615      * Sets the individual  score cutoff values (for example, gathering
 616      * thresholds from Pfam). Domain ids are the keys, cutoffs the values.
 617      *
 618      * @param individual_score_cutoffs
 619      */
 620     public void setIndividualScoreCutoffs( final Map<String, Double> individual_score_cutoffs ) {
 621         _individual_score_cutoffs = individual_score_cutoffs;
 622     }
 623
 624     public void setMaxAllowedOverlap( final int max_allowed_overlap ) {
 625         if ( max_allowed_overlap < 0 ) {
 626             throw new IllegalArgumentException( "Attempt to set max allowed overlap to less than zero." );
 627         }
 628         _max_allowed_overlap = max_allowed_overlap;
 629     }
 630
 631     private void setProteinsEncountered( final int proteins_encountered ) {
 632         _proteins_encountered = proteins_encountered;
 633     }
 634
 635     private void setProteinsIgnoredDueToFilter( final int proteins_ignored_due_to_filter ) {
 636         _proteins_ignored_due_to_filter = proteins_ignored_due_to_filter;
 637     }
 638
 639     private void setProteinsStored( final int proteins_stored ) {
 640         _proteins_stored = proteins_stored;
 641     }
 642
 643     public void setReturnType( final ReturnType return_type ) {
 644         _return_type = return_type;
 645     }
 646
 647     private void setTime( final long time ) {
 648         _time = time;
 649     }
 650
 651     public static enum FilterType {
 652         NONE, POSITIVE_PROTEIN, NEGATIVE_PROTEIN, NEGATIVE_DOMAIN
 653     }
 654
 655     static public enum INDIVIDUAL_SCORE_CUTOFF {
 656         FULL_SEQUENCE, DOMAIN, NONE;
 657     }
 658
 659     public static enum ReturnType {
 660         UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN
 661     }
 662 }