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.BasicProtein;
45 import org.forester.protein.Domain;
46 import org.forester.protein.DomainId;
47 import org.forester.protein.Protein;
48 import org.forester.surfacing.BasicDomain;
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 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;
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 private final boolean _allow_proteins_with_same_name;
96 public HmmscanPerDomainTableParser( final File input_file,
98 final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
99 _input_file = input_file;
102 _filter_type = FilterType.NONE;
103 _ind_cutoff = individual_cutoff_applies_to;
104 _allow_proteins_with_same_name = false;
108 public HmmscanPerDomainTableParser( final File input_file,
109 final String species,
110 final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
111 final boolean allow_proteins_with_same_name ) {
112 _input_file = input_file;
115 _filter_type = FilterType.NONE;
116 _ind_cutoff = individual_cutoff_applies_to;
117 _allow_proteins_with_same_name = allow_proteins_with_same_name;
121 public HmmscanPerDomainTableParser( final File input_file,
122 final String species,
123 final Set<DomainId> filter,
124 final FilterType filter_type,
125 final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to ) {
126 _input_file = input_file;
129 _filter_type = filter_type;
130 _ind_cutoff = individual_cutoff_applies_to;
131 _allow_proteins_with_same_name = false;
135 public HmmscanPerDomainTableParser( final File input_file,
136 final String species,
137 final Set<DomainId> filter,
138 final FilterType filter_type,
139 final INDIVIDUAL_SCORE_CUTOFF individual_cutoff_applies_to,
140 final boolean allow_proteins_with_same_name ) {
141 _input_file = input_file;
144 _filter_type = filter_type;
145 _ind_cutoff = individual_cutoff_applies_to;
146 _allow_proteins_with_same_name = allow_proteins_with_same_name;
150 public boolean isAllowProteinsWithSameName() {
151 return _allow_proteins_with_same_name;
154 private void actuallyAddProtein( final List<Protein> proteins, final Protein current_protein ) {
155 final List<Domain> l = current_protein.getProteinDomains();
156 for( final Domain d : l ) {
157 getDomainsStoredSet().add( d.getDomainId() );
159 proteins.add( current_protein );
163 private void addProtein( final List<Protein> proteins, Protein current_protein ) {
164 if ( ( getMaxAllowedOverlap() != HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT )
165 || isIgnoreEngulfedDomains() ) {
166 final int domains_count = current_protein.getNumberOfProteinDomains();
167 current_protein = SurfacingUtil.removeOverlappingDomains( getMaxAllowedOverlap(),
168 isIgnoreEngulfedDomains(),
170 final int domains_removed = domains_count - current_protein.getNumberOfProteinDomains();
171 _domains_stored -= domains_removed;
172 _domains_ignored_due_to_overlap += domains_removed;
174 if ( ( getFilterType() == FilterType.POSITIVE_PROTEIN ) || ( getFilterType() == FilterType.NEGATIVE_PROTEIN ) ) {
175 final Set<DomainId> domain_ids_in_protein = new HashSet<DomainId>();
176 for( final Domain d : current_protein.getProteinDomains() ) {
177 domain_ids_in_protein.add( d.getDomainId() );
179 domain_ids_in_protein.retainAll( getFilter() );
180 if ( getFilterType() == FilterType.POSITIVE_PROTEIN ) {
181 if ( domain_ids_in_protein.size() > 0 ) {
182 actuallyAddProtein( proteins, current_protein );
185 ++_proteins_ignored_due_to_filter;
189 if ( domain_ids_in_protein.size() < 1 ) {
190 actuallyAddProtein( proteins, current_protein );
193 ++_proteins_ignored_due_to_filter;
198 actuallyAddProtein( proteins, current_protein );
202 public int getDomainsEncountered() {
203 return _domains_encountered;
206 public int getDomainsIgnoredDueToDuf() {
207 return _domains_ignored_due_to_duf;
210 public int getDomainsIgnoredDueToEval() {
211 return _domains_ignored_due_to_e_value;
214 public int getDomainsIgnoredDueToIndividualScoreCutoff() {
215 return _domains_ignored_due_to_individual_score_cutoff;
218 public int getDomainsIgnoredDueToNegativeDomainFilter() {
219 return _domains_ignored_due_to_negative_domain_filter;
222 public Map<String, Integer> getDomainsIgnoredDueToNegativeDomainFilterCountsMap() {
223 return _domains_ignored_due_to_negative_domain_filter_counts_map;
226 public int getDomainsIgnoredDueToOverlap() {
227 return _domains_ignored_due_to_overlap;
230 public Map<String, Integer> getDomainsIgnoredDueToVirusLikeIdCountsMap() {
231 return _domains_ignored_due_to_virus_like_id_counts_map;
234 public int getDomainsIgnoredDueToVirusLikeIds() {
235 return _domains_ignored_due_to_virus_like_id;
238 public int getDomainsStored() {
239 return _domains_stored;
242 public SortedSet<DomainId> getDomainsStoredSet() {
243 return _domains_stored_set;
246 private double getEValueMaximum() {
247 return _e_value_maximum;
250 private Set<DomainId> getFilter() {
254 private FilterType getFilterType() {
258 public INDIVIDUAL_SCORE_CUTOFF getIndividualCutoffAppliesTo() {
262 private Map<String, Double> getIndividualScoreCutoffs() {
263 return _individual_score_cutoffs;
266 private File getInputFile() {
270 private int getMaxAllowedOverlap() {
271 return _max_allowed_overlap;
274 public int getProteinsEncountered() {
275 return _proteins_encountered;
278 public int getProteinsIgnoredDueToFilter() {
279 return _proteins_ignored_due_to_filter;
282 public int getProteinsStored() {
283 return _proteins_stored;
286 private ReturnType getReturnType() {
290 private String getSpecies() {
294 public long getTime() {
298 private void init() {
299 _e_value_maximum = HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT;
300 setIgnoreDufs( HmmscanPerDomainTableParser.IGNORE_DUFS_DEFAULT );
301 setReturnType( HmmscanPerDomainTableParser.RETURN_TYPE_DEFAULT );
302 _max_allowed_overlap = HmmscanPerDomainTableParser.MAX_ALLOWED_OVERLAP_DEFAULT;
303 setIndividualScoreCutoffs( null );
304 setIgnoreEngulfedDomains( false );
305 setIgnoreVirusLikeIds( false );
309 private void intitCounts() {
310 setDomainsStoredSet( new TreeSet<DomainId>() );
311 setDomainsEncountered( 0 );
312 setProteinsEncountered( 0 );
313 setProteinsIgnoredDueToFilter( 0 );
314 setDomainsIgnoredDueToNegativeFilter( 0 );
315 setDomainsIgnoredDueToDuf( 0 );
316 setDomainsIgnoredDueToEval( 0 );
317 setDomainsIgnoredDueToIndividualScoreCutoff( 0 );
318 setDomainsIgnoredDueToVirusLikeId( 0 );
319 setDomainsIgnoredDueToOverlap( 0 );
320 setDomainsStored( 0 );
321 setProteinsStored( 0 );
323 setDomainsIgnoredDueToVirusLikeIdCountsMap( new TreeMap<String, Integer>() );
324 setDomainsIgnoredDueToNegativeDomainFilterCountsMap( new TreeMap<String, Integer>() );
327 private boolean isIgnoreDufs() {
331 private boolean isIgnoreEngulfedDomains() {
332 return _ignore_engulfed_domains;
335 private boolean isIgnoreVirusLikeIds() {
336 return _ignore_virus_like_ids;
339 public List<Protein> parse() throws IOException {
340 if ( ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.NONE )
341 && ( ( getIndividualScoreCutoffs() == null ) || ( getIndividualScoreCutoffs().size() < 1 ) ) ) {
342 throw new RuntimeException( "attempt to use individual cuttoffs with having set them" );
345 final Set<String> prev_queries = new HashSet<String>();
346 final String error = ForesterUtil.isReadableFile( getInputFile() );
347 if ( !ForesterUtil.isEmpty( error ) ) {
348 throw new IOException( error );
350 final BufferedReader br = new BufferedReader( new FileReader( getInputFile() ) );
352 final List<Protein> proteins = new ArrayList<Protein>();
353 Protein current_protein = null;
355 final long start_time = new Date().getTime();
356 String prev_query = "";
358 while ( ( line = br.readLine() ) != null ) {
360 if ( ForesterUtil.isEmpty( line ) || line.startsWith( "#" ) ) {
363 // 0 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22
364 // # --- full sequence --- -------------- this domain ------------- hmm coord ali coord env coord
365 // # 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
366 // #------------------- ---------- ----- -------------------- ---------- ----- --------- ------ ----- --- --- --------- --------- ------ ----- ----- ----- ----- ----- ----- ----- ---- ---------------------
367 // 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
368 // 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
369 // 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
370 // 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
371 // 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
372 final String tokens[] = line.split( "\\s+" );
373 final String target_id = tokens[ 0 ];
374 final String target_acc = tokens[ 1 ];
375 final int tlen = parseInt( tokens[ 2 ], line_number, "tlen" );
376 final String query = tokens[ 3 ];
377 final String query_acc = tokens[ 4 ];
378 final int qlen = parseInt( tokens[ 5 ], line_number, "qlen" );
379 final double fs_e_value = parseDouble( tokens[ 6 ], line_number, "E-value" );
380 final double fs_score = parseDouble( tokens[ 7 ], line_number, "score" );
381 final int domain_number = parseInt( tokens[ 9 ], line_number, "count" );
382 final int total_domains = parseInt( tokens[ 10 ], line_number, "total" );
383 final double c_e_value = parseDouble( tokens[ 11 ], line_number, "c-Evalue" );
384 final double i_e_value = parseDouble( tokens[ 12 ], line_number, "i-Evalue" );
385 final double domain_score = parseDouble( tokens[ 13 ], line_number, "score" );
386 final int hmm_from = parseInt( tokens[ 15 ], line_number, "hmm from" );
387 final int hmm_to = parseInt( tokens[ 16 ], line_number, "hmm to" );
388 final int ali_from = parseInt( tokens[ 17 ], line_number, "ali from" );
389 final int ali_to = parseInt( tokens[ 18 ], line_number, "ali to" );
390 final int env_from = parseInt( tokens[ 19 ], line_number, "env from" );
391 final int env_to = parseInt( tokens[ 20 ], line_number, "env to" );
392 ++_domains_encountered;
393 if ( !query.equals( prev_query ) || ( qlen != prev_qlen ) ) {
394 if ( !isAllowProteinsWithSameName() ) {
395 if ( query.equals( prev_query ) ) {
396 throw new IOException( "more than one protein named [" + query + "]" + " lengths: " + qlen
397 + ", " + prev_qlen );
399 if ( prev_queries.contains( query ) ) {
400 throw new IOException( "more than one protein named [" + query + "]" );
405 prev_queries.add( query );
406 if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
407 addProtein( proteins, current_protein );
409 if ( getReturnType() == ReturnType.UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN ) {
410 current_protein = new BasicProtein( query, getSpecies(), qlen );
413 throw new IllegalArgumentException( "unknown return type" );
416 boolean failed_cutoff = false;
417 if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.NONE ) {
418 if ( getIndividualScoreCutoffs().containsKey( target_id ) ) {
419 final double cutoff = getIndividualScoreCutoffs().get( target_id );
420 if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.FULL_SEQUENCE ) {
421 if ( fs_score < cutoff ) {
422 failed_cutoff = true;
425 else if ( getIndividualCutoffAppliesTo() != INDIVIDUAL_SCORE_CUTOFF.DOMAIN ) {
426 if ( domain_score < cutoff ) {
427 failed_cutoff = true;
432 throw new IOException( "could not find a score cutoff value for domain id \"" + target_id
433 + "\" [line " + line_number + "] in [" + getInputFile().getCanonicalPath() + "]" );
436 final String uc_id = target_id.toUpperCase();
437 if ( failed_cutoff ) {
438 ++_domains_ignored_due_to_individual_score_cutoff;
440 else if ( ali_from == ali_to ) {
443 else if ( ( getEValueMaximum() != HmmscanPerDomainTableParser.E_VALUE_MAXIMUM_DEFAULT )
444 && ( fs_e_value > getEValueMaximum() ) ) {
445 ++_domains_ignored_due_to_e_value;
447 else if ( isIgnoreDufs() && uc_id.startsWith( "DUF" ) ) {
448 ++_domains_ignored_due_to_duf;
450 else if ( isIgnoreVirusLikeIds()
451 && ( uc_id.contains( VIR ) || uc_id.contains( PHAGE ) || uc_id.contains( RETRO )
452 || uc_id.contains( TRANSPOS ) || uc_id.startsWith( RV ) || uc_id.startsWith( GAG )
453 || uc_id.startsWith( HCV ) || uc_id.startsWith( HERPES ) || uc_id.startsWith( BACULO ) ) ) {
454 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToVirusLikeIdCountsMap(), target_id );
455 ++_domains_ignored_due_to_virus_like_id;
457 else if ( ( getFilterType() == FilterType.NEGATIVE_DOMAIN )
458 && getFilter().contains( new DomainId( target_id ) ) ) {
459 ++_domains_ignored_due_to_negative_domain_filter;
460 ForesterUtil.increaseCountingMap( getDomainsIgnoredDueToNegativeDomainFilterCountsMap(), target_id );
464 final Domain pd = new BasicDomain( target_id,
467 ( short ) domain_number,
468 ( short ) total_domains,
473 current_protein.addProteinDomain( pd );
475 catch ( final IllegalArgumentException e ) {
476 throw new IOException( "problem with domain parsing at line " + line_number + "[" + line + "]: "
481 } // while ( ( line = br.readLine() ) != null )
482 if ( ( current_protein != null ) && ( current_protein.getProteinDomains().size() > 0 ) ) {
483 addProtein( proteins, current_protein );
485 setProteinsEncountered( prev_queries.size() );
486 setTime( new Date().getTime() - start_time );
490 private double parseDouble( final String double_str, final int line_number, final String label ) throws IOException {
493 d = Double.valueOf( double_str ).doubleValue();
495 catch ( final NumberFormatException e ) {
496 throw new IOException( "could not parse \" +label + \" from \"" + double_str + "\" [line " + line_number
497 + "] in [" + getInputFile().getCanonicalPath() + "]" );
502 private int parseInt( final String double_str, final int line_number, final String label ) throws IOException {
505 i = Integer.valueOf( double_str ).intValue();
507 catch ( final NumberFormatException e ) {
508 throw new IOException( "could not parse \"" + label + "\" from \"" + double_str + "\" [line " + line_number
509 + "] in [" + getInputFile().getCanonicalPath() + "]" );
514 private void setDomainsEncountered( final int domains_encountered ) {
515 _domains_encountered = domains_encountered;
518 private void setDomainsIgnoredDueToDuf( final int domains_ignored_due_to_duf ) {
519 _domains_ignored_due_to_duf = domains_ignored_due_to_duf;
522 private void setDomainsIgnoredDueToEval( final int domains_ignored_due_to_e_value ) {
523 _domains_ignored_due_to_e_value = domains_ignored_due_to_e_value;
526 private void setDomainsIgnoredDueToIndividualScoreCutoff( final int domains_ignored_due_to_individual_score_cutoff ) {
527 _domains_ignored_due_to_individual_score_cutoff = domains_ignored_due_to_individual_score_cutoff;
530 private void setDomainsIgnoredDueToNegativeDomainFilterCountsMap( final Map<String, Integer> domains_ignored_due_to_negative_domain_filter_counts_map ) {
531 _domains_ignored_due_to_negative_domain_filter_counts_map = domains_ignored_due_to_negative_domain_filter_counts_map;
534 private void setDomainsIgnoredDueToNegativeFilter( final int domains_ignored_due_to_negative_domain_filter ) {
535 _domains_ignored_due_to_negative_domain_filter = domains_ignored_due_to_negative_domain_filter;
538 private void setDomainsIgnoredDueToOverlap( final int domains_ignored_due_to_overlap ) {
539 _domains_ignored_due_to_overlap = domains_ignored_due_to_overlap;
542 private void setDomainsIgnoredDueToVirusLikeId( final int i ) {
543 _domains_ignored_due_to_virus_like_id = i;
546 private void setDomainsIgnoredDueToVirusLikeIdCountsMap( final Map<String, Integer> domains_ignored_due_to_virus_like_id_counts_map ) {
547 _domains_ignored_due_to_virus_like_id_counts_map = domains_ignored_due_to_virus_like_id_counts_map;
550 private void setDomainsStored( final int domains_stored ) {
551 _domains_stored = domains_stored;
554 private void setDomainsStoredSet( final SortedSet<DomainId> _storeddomains_stored ) {
555 _domains_stored_set = _storeddomains_stored;
558 public void setEValueMaximum( final double e_value_maximum ) {
559 if ( e_value_maximum < 0.0 ) {
560 throw new IllegalArgumentException( "attempt to set the maximum E-value to a negative value" );
562 _e_value_maximum = e_value_maximum;
565 public void setIgnoreDufs( final boolean ignore_dufs ) {
566 _ignore_dufs = ignore_dufs;
570 * To ignore domains which are completely engulfed by domains (individual
571 * ones or stretches of overlapping ones) with better support values.
574 * @param ignored_engulfed_domains
576 public void setIgnoreEngulfedDomains( final boolean ignore_engulfed_domains ) {
577 _ignore_engulfed_domains = ignore_engulfed_domains;
580 public void setIgnoreVirusLikeIds( final boolean ignore_virus_like_ids ) {
581 _ignore_virus_like_ids = ignore_virus_like_ids;
585 * Sets the individual score cutoff values (for example, gathering
586 * thresholds from Pfam). Domain ids are the keys, cutoffs the values.
588 * @param individual_score_cutoffs
590 public void setIndividualScoreCutoffs( final Map<String, Double> individual_score_cutoffs ) {
591 _individual_score_cutoffs = individual_score_cutoffs;
594 public void setMaxAllowedOverlap( final int max_allowed_overlap ) {
595 if ( max_allowed_overlap < 0 ) {
596 throw new IllegalArgumentException( "Attempt to set max allowed overlap to less than zero." );
598 _max_allowed_overlap = max_allowed_overlap;
601 private void setProteinsEncountered( final int proteins_encountered ) {
602 _proteins_encountered = proteins_encountered;
605 private void setProteinsIgnoredDueToFilter( final int proteins_ignored_due_to_filter ) {
606 _proteins_ignored_due_to_filter = proteins_ignored_due_to_filter;
609 private void setProteinsStored( final int proteins_stored ) {
610 _proteins_stored = proteins_stored;
613 public void setReturnType( final ReturnType return_type ) {
614 _return_type = return_type;
617 private void setTime( final long time ) {
621 public static enum FilterType {
622 NONE, POSITIVE_PROTEIN, NEGATIVE_PROTEIN, NEGATIVE_DOMAIN
625 static public enum INDIVIDUAL_SCORE_CUTOFF {
626 FULL_SEQUENCE, DOMAIN, NONE;
629 public static enum ReturnType {
630 UNORDERED_PROTEIN_DOMAIN_COLLECTION_PER_PROTEIN