4 // FORESTER -- software libraries and applications
5 // for evolutionary biology research and applications.
7 // Copyright (C) 2008-2009 Christian M. Zmasek
8 // Copyright (C) 2008-2009 Burnham Institute for Medical Research
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.
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.
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
25 // Contact: phylosoft @ gmail . com
26 // WWW: www.phylosoft.org/forester
28 package org.forester.io.parsers;
30 import java.io.BufferedReader;
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;
40 import java.util.SortedSet;
41 import java.util.TreeMap;
42 import java.util.TreeSet;
44 import org.forester.protein.BasicDomain;
45 import org.forester.protein.BasicProtein;
46 import org.forester.protein.Domain;
47 import org.forester.protein.DomainId;
48 import org.forester.protein.Protein;
49 import org.forester.surfacing.SurfacingUtil;
50 import org.forester.util.ForesterUtil;
52 public final class HmmscanPerDomainTableParser {
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 static final boolean IGNORE_REPLACED_RRMS = true;
68 private final Set<DomainId> _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<DomainId> _domains_stored_set;
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;
97 public HmmscanPerDomainTableParser( final File input_file,
99 final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
100 _input_file = input_file;
103 _filter_type = FilterType.NONE;
104 _ind_cutoff = individual_cutoff_applies_to;
105 _allow_proteins_with_same_name = false;
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;
116 _filter_type = FilterType.NONE;
117 _ind_cutoff = individual_cutoff_applies_to;
118 _allow_proteins_with_same_name = allow_proteins_with_same_name;
122 public HmmscanPerDomainTableParser( final File input_file,
123 final String species,
124 final Set<DomainId> filter,
125 final FilterType filter_type,
126 final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
127 _input_file = input_file;
130 _filter_type = filter_type;
131 _ind_cutoff = individual_cutoff_applies_to;
132 _allow_proteins_with_same_name = false;
136 public HmmscanPerDomainTableParser( final File input_file,
137 final String species,
138 final Set<DomainId> 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;
145 _filter_type = filter_type;
146 _ind_cutoff = individual_cutoff_applies_to;
147 _allow_proteins_with_same_name = allow_proteins_with_same_name;
151 public boolean isAllowProteinsWithSameName() {
152 return _allow_proteins_with_same_name;
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() );
160 proteins.add( current_protein );
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(),
171 final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
172 _domains_stored -= domains_removed;
173 _domains_ignored_due_to_overlap += domains_removed;
175 if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
176 final Set<DomainId> domain_ids_in_protein = new HashSet<DomainId>();
177 for( final Domain d : current_protein.getProteinDomains() ) {
178 domain_ids_in_protein.add( d.getDomainId() );
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 );
186 ++_proteins_ignored_due_to_filter;
190 if ( domain_ids_in_protein.size() < 1 ) {
191 actuallyAddProtein( proteins, current_protein );
194 ++_proteins_ignored_due_to_filter;
199 actuallyAddProtein( proteins, current_protein );
203 public int getDomainsEncountered() {
204 return _domains_encountered;
207 public int getDomainsIgnoredDueToDuf() {
208 return _domains_ignored_due_to_duf;
211 public int getDomainsIgnoredDueToEval() {
212 return _domains_ignored_due_to_e_value;
215 public int getDomainsIgnoredDueToIndividualScoreCutoff() {
216 return _domains_ignored_due_to_individual_score_cutoff;
219 public int getDomainsIgnoredDueToNegativeDomainFilter() {
220 return _domains_ignored_due_to_negative_domain_filter;
223 public Map<String, Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap() {
224 return _domains_ignored_due_to_negative_domain_filter_counts_map;
227 public int getDomainsIgnoredDueToOverlap() {
228 return _domains_ignored_due_to_overlap;
231 public Map<String, Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap() {
232 return _domains_ignored_due_to_virus_like_id_counts_map;
235 public int getDomainsIgnoredDueToVirusLikeIds() {
236 return _domains_ignored_due_to_virus_like_id;
239 public int getDomainsStored() {
240 return _domains_stored;
243 public SortedSet<DomainId> getDomainsStoredSet() {
244 return _domains_stored_set;
247 private double getEValueMaximum() {
248 return _e_value_maximum;
251 private Set<DomainId> getFilter() {
255 private FilterType getFilterType() {
259 public INDIVIDUAL_SCORE_CUTOFF getIndividualCutoffAppliesTo() {
263 private Map<String, Double> getIndividualScoreCutoffs() {
264 return _individual_score_cutoffs;
267 private File getInputFile() {
271 private int getMaxAllowedOverlap() {
272 return _max_allowed_overlap;
275 public int getProteinsEncountered() {
276 return _proteins_encountered;
279 public int getProteinsIgnoredDueToFilter() {
280 return _proteins_ignored_due_to_filter;
283 public int getProteinsStored() {
284 return _proteins_stored;
287 private ReturnType getReturnType() {
291 private String getSpecies() {
295 public long getTime() {
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 );
310 private void intitCounts() {
311 setDomainsStoredSet( new TreeSet<DomainId>() );
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 );
324 setDomainsIgnoredDueToVirusLikeIdCountsMap( new TreeMap<String, Integer>() );
325 setDomainsIgnoredDueToNegativeDomainFilterCountsMap( new TreeMap<String, Integer>() );
328 private boolean isIgnoreDufs() {
332 private boolean isIgnoreEngulfedDomains() {
333 return _ignore_engulfed_domains;
336 private boolean isIgnoreVirusLikeIds() {
337 return _ignore_virus_like_ids;
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" );
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 );
351 final BufferedReader br = new BufferedReader( new FileReader( getInputFile() ) );
353 final List<Protein> proteins = new ArrayList<Protein>();
354 Protein current_protein = null;
356 final long start_time = new Date().getTime();
357 String prev_query = "";
359 while ( ( line = br.readLine() ) != null ) {
361 if ( ForesterUtil.isEmpty( line ) || line.startsWith( "#" ) ) {
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 );
400 if ( prev_queries.contains( query ) ) {
401 throw new IOException( "more than one protein named [" + query + "]" );
406 prev_queries.add( query );
407 if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
408 addProtein( proteins, current_protein );
410 if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
411 current_protein = new BasicProtein( query, getSpecies(), qlen );
414 throw new IllegalArgumentException( "unknown return type" );
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;
426 else if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.DOMAIN ) {
427 if ( domain_score < cutoff ) {
428 failed_cutoff = true;
433 throw new IOException( "could not find a score cutoff value for domain id \"" + target_id
434 + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
437 final String uc_id = target_id.toUpperCase();
438 if ( failed_cutoff ) {
439 ++_domains_ignored_due_to_individual_score_cutoff;
441 else if ( ali_from == ali_to ) {
444 else if ( ( getEValueMaximum() != HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT )
445 && ( fs_e_value > getEValueMaximum() ) ) {
446 ++_domains_ignored_due_to_e_value;
448 else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) {
449 ++_domains_ignored_due_to_duf;
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" ) ) ) {
455 else if ( isIgnoreVirusLikeIds()
456 && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
457 || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )
458 || uc_id.startsWith( HCV ) || uc_id.startsWith( HERPES ) || uc_id.startsWith( BACULO ) ) ) {
459 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), target_id );
460 ++_domains_ignored_due_to_virus_like_id;
462 else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN )
463 && getFilter().contains( new DomainId( target_id ) ) ) {
464 ++_domains_ignored_due_to_negative_domain_filter;
465 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), target_id );
469 final Domain pd = new BasicDomain( target_id,
472 ( short ) domain_number,
473 ( short ) total_domains,
478 current_protein.addProteinDomain( pd );
480 catch ( final IllegalArgumentException e ) {
481 throw new IOException( "problem with domain parsing at line " + line_number + "[" + line + "]: "
486 } // while ( ( line = br.readLine() ) != null )
487 if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
488 addProtein( proteins, current_protein );
490 setProteinsEncountered( prev_queries.size() );
491 setTime( new Date().getTime() - start_time );
495 private double parseDouble( final String double_str, final int line_number, final String label ) throws IOException {
498 d = Double.valueOf( double_str ).doubleValue();
500 catch ( final NumberFormatException e ) {
501 throw new IOException( "could not parse \" +label + \" from \"" + double_str + "\" [line " + line_number
502 + "] in [" + getInputFile().getCanonicalPath() + "]" );
507 private int parseInt( final String double_str, final int line_number, final String label ) throws IOException {
510 i = Integer.valueOf( double_str ).intValue();
512 catch ( final NumberFormatException e ) {
513 throw new IOException( "could not parse \"" + label + "\" from \"" + double_str + "\" [line " + line_number
514 + "] in [" + getInputFile().getCanonicalPath() + "]" );
519 private void setDomainsEncountered( final int domains_encountered ) {
520 _domains_encountered = domains_encountered;
523 private void setDomainsIgnoredDueToDuf( final int domains_ignored_due_to_duf ) {
524 _domains_ignored_due_to_duf = domains_ignored_due_to_duf;
527 private void setDomainsIgnoredDueToEval( final int domains_ignored_due_to_e_value ) {
528 _domains_ignored_due_to_e_value = domains_ignored_due_to_e_value;
531 private void setDomainsIgnoredDueToIndividualScoreCutoff( final int domains_ignored_due_to_individual_score_cutoff ) {
532 _domains_ignored_due_to_individual_score_cutoff = domains_ignored_due_to_individual_score_cutoff;
535 private void setDomainsIgnoredDueToNegativeDomainFilterCountsMap( final Map<String, Integer> domains_ignored_due_to_negative_domain_filter_counts_map ) {
536 _domains_ignored_due_to_negative_domain_filter_counts_map = domains_ignored_due_to_negative_domain_filter_counts_map;
539 private void setDomainsIgnoredDueToNegativeFilter( final int domains_ignored_due_to_negative_domain_filter ) {
540 _domains_ignored_due_to_negative_domain_filter = domains_ignored_due_to_negative_domain_filter;
543 private void setDomainsIgnoredDueToOverlap( final int domains_ignored_due_to_overlap ) {
544 _domains_ignored_due_to_overlap = domains_ignored_due_to_overlap;
547 private void setDomainsIgnoredDueToVirusLikeId( final int i ) {
548 _domains_ignored_due_to_virus_like_id = i;
551 private void setDomainsIgnoredDueToVirusLikeIdCountsMap( final Map<String, Integer> domains_ignored_due_to_virus_like_id_counts_map ) {
552 _domains_ignored_due_to_virus_like_id_counts_map = domains_ignored_due_to_virus_like_id_counts_map;
555 private void setDomainsStored( final int domains_stored ) {
556 _domains_stored = domains_stored;
559 private void setDomainsStoredSet( final SortedSet<DomainId> _storeddomains_stored ) {
560 _domains_stored_set = _storeddomains_stored;
563 public void setEValueMaximum( final double e_value_maximum ) {
564 if ( e_value_maximum < 0.0 ) {
565 throw new IllegalArgumentException( "attempt to set the maximum E-value to a negative value" );
567 _e_value_maximum = e_value_maximum;
570 public void setIgnoreDufs( final boolean ignore_dufs ) {
571 _ignore_dufs = ignore_dufs;
575 * To ignore domains which are completely engulfed by domains (individual
576 * ones or stretches of overlapping ones) with better support values.
579 * @param ignored_engulfed_domains
581 public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) {
582 _ignore_engulfed_domains = ignore_engulfed_domains;
585 public void setIgnoreVirusLikeIds( final boolean ignore_virus_like_ids ) {
586 _ignore_virus_like_ids = ignore_virus_like_ids;
590 * Sets the individual score cutoff values (for example, gathering
591 * thresholds from Pfam). Domain ids are the keys, cutoffs the values.
593 * @param individual_score_cutoffs
595 public void setIndividualScoreCutoffs( final Map<String, Double> individual_score_cutoffs ) {
596 _individual_score_cutoffs = individual_score_cutoffs;
599 public void setMaxAllowedOverlap( final int max_allowed_overlap ) {
600 if ( max_allowed_overlap < 0 ) {
601 throw new IllegalArgumentException( "Attempt to set max allowed overlap to less than zero." );
603 _max_allowed_overlap = max_allowed_overlap;
606 private void setProteinsEncountered( final int proteins_encountered ) {
607 _proteins_encountered = proteins_encountered;
610 private void setProteinsIgnoredDueToFilter( final int proteins_ignored_due_to_filter ) {
611 _proteins_ignored_due_to_filter = proteins_ignored_due_to_filter;
614 private void setProteinsStored( final int proteins_stored ) {
615 _proteins_stored = proteins_stored;
618 public void setReturnType( final ReturnType return_type ) {
619 _return_type = return_type;
622 private void setTime( final long time ) {
626 public static enum FilterType {
627 NONE, POSITIVE_PROTEIN, NEGATIVE_PROTEIN, NEGATIVE_DOMAIN
630 static public enum INDIVIDUAL_SCORE_CUTOFF {
631 FULL_SEQUENCE, DOMAIN, NONE;
634 public static enum ReturnType {
635 UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN