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