37 #include <OpenMS/config.h> 53 #include <unordered_set> 100 template <
class HitType>
110 higher_score_better(higher_score_better_)
115 if (higher_score_better)
117 return hit.getScore() >= score;
119 return hit.getScore() <= score;
128 template <
class HitType>
140 throw Exception::IllegalArgument(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"The cut-off value for rank filtering must not be zero!");
146 Size hit_rank = hit.getRank();
151 return hit_rank <= rank;
160 template <
class HitType>
176 if (found.
isEmpty())
return false;
177 if (value.
isEmpty())
return true;
178 return found == value;
183 template <
class HitType>
199 if (found.
isEmpty())
return false;
200 return double(found) <= value;
205 template <
class HitType>
213 target_decoy(
"target_decoy",
"decoy"), is_decoy(
"isDecoy",
"true")
221 return target_decoy(hit) || is_decoy(hit);
230 template <
class HitType>
238 accessions(accessions_)
245 if (accessions.count(it) > 0)
return true;
266 template <
class HitType>
274 accessions(accessions_)
281 if (accessions.count(it) > 0)
return true;
302 template <
class HitType,
class Entry>
311 for(
typename std::vector<Entry>::iterator rec_it = records.begin();
312 rec_it != records.end(); ++rec_it)
314 items[getKey(*rec_it)] = &(*rec_it);
327 return items.count(getHitKey(hit)) > 0;
337 if(!exists(evidence)){
338 throw Exception::InvalidParameter(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Accession: '"+ getHitKey(evidence) +
"'. peptide evidence accession not in data");
340 return *(items.find(getHitKey(evidence))->second);
356 struct HasMinPeptideLength;
362 struct HasLowMZError;
369 struct HasMatchingModification;
376 struct HasMatchingSequence;
379 struct HasNoEvidence;
397 digestion_(digestion), min_cleavages_(min), max_cleavages_(max)
408 [&](
const Int missed_cleavages)
411 bool max_filter = max_cleavages_ != disabledValue() ?
412 missed_cleavages > max_cleavages_ :
false;
413 bool min_filter = min_cleavages_ != disabledValue() ?
414 missed_cleavages < min_cleavages_ :
false;
415 return max_filter || min_filter;
421 hits.erase(std::remove_if(hits.begin(), hits.end(), (*this)),
445 bool ignore_missed_cleavages,
446 bool methionine_cleavage) :
447 accession_resolver_(entries),
448 digestion_(digestion),
449 ignore_missed_cleavages_(ignore_missed_cleavages),
450 methionine_cleavage_(methionine_cleavage)
461 if (accession_resolver_.
exists(evidence))
465 evidence.
getStart(), evidence.
getEnd() - evidence.
getStart(), ignore_missed_cleavages_, methionine_cleavage_);
471 OPENMS_LOG_WARN <<
"Peptide accession not available! Skipping Evidence." << std::endl;
476 <<
"' not found in fasta file!" << std::endl;
484 IDFilter::FilterPeptideEvidences<IDFilter::DigestionFilter>(*
this,peptides);
496 template <
class IdentificationType>
503 return id.getHits().empty();
530 template <
class Container,
class Predicate>
533 items.erase(std::remove_if(items.begin(), items.end(), pred),
538 template <
class Container,
class Predicate>
541 items.erase(std::remove_if(items.begin(), items.end(), std::not1(pred)),
546 template <
class IDContainer,
class Predicate>
549 for (
auto& item : items)
551 removeMatchingItems(item.getHits(), pred);
556 template <
class IDContainer,
class Predicate>
559 for (
auto& item : items)
561 keepMatchingItems(item.getHits(), pred);
565 template <
class MapType,
class Predicate>
568 for (
auto& feat : prot_and_pep_ids)
570 keepMatchingItemsUnroll(feat.getPeptideIdentifications(), pred);
572 keepMatchingItemsUnroll(prot_and_pep_ids.getUnassignedPeptideIdentifications(), pred);
575 template <
class MapType,
class Predicate>
578 for (
auto& feat : prot_and_pep_ids)
580 removeMatchingItemsUnroll(feat.getPeptideIdentifications(), pred);
582 removeMatchingItemsUnroll(prot_and_pep_ids.getUnassignedPeptideIdentifications(), pred);
592 template <
class IdentificationType>
596 for (
typename std::vector<IdentificationType>::const_iterator id_it =
597 ids.begin(); id_it != ids.end(); ++id_it)
599 counter += id_it->getHits().size();
616 template <
class IdentificationType>
618 const std::vector<IdentificationType>& identifications,
619 bool assume_sorted,
typename IdentificationType::HitType& best_hit)
621 if (identifications.empty())
return false;
623 typename std::vector<IdentificationType>::const_iterator best_id_it =
624 identifications.end();
625 typename std::vector<typename IdentificationType::HitType>::const_iterator
628 for (
typename std::vector<IdentificationType>::const_iterator id_it =
629 identifications.begin(); id_it != identifications.end(); ++id_it)
631 if (id_it->getHits().empty())
continue;
633 if (best_id_it == identifications.end())
636 best_hit_it = id_it->getHits().begin();
638 else if (best_id_it->getScoreType() != id_it->getScoreType())
640 throw Exception::InvalidValue(__FILE__, __LINE__, OPENMS_PRETTY_FUNCTION,
"Can't compare scores of different types", best_id_it->getScoreType() +
"/" + id_it->getScoreType());
643 bool higher_better = best_id_it->isHigherScoreBetter();
644 for (
typename std::vector<typename IdentificationType::HitType>::
645 const_iterator hit_it = id_it->getHits().begin(); hit_it !=
646 id_it->getHits().end(); ++hit_it)
648 if ((higher_better && (hit_it->getScore() >
649 best_hit_it->getScore())) ||
650 (!higher_better && (hit_it->getScore() <
651 best_hit_it->getScore())))
653 best_hit_it = hit_it;
655 if (assume_sorted)
break;
659 if (best_id_it == identifications.end())
664 best_hit = *best_hit_it;
675 static void extractPeptideSequences(
676 const std::vector<PeptideIdentification>& peptides,
677 std::set<String>& sequences,
bool ignore_mods =
false);
685 template<
class Ev
idenceFilter>
687 EvidenceFilter& filter,
688 std::vector<PeptideIdentification>& peptides)
690 for(std::vector<PeptideIdentification>::iterator pep_it = peptides.begin();
691 pep_it != peptides.end(); ++pep_it)
693 for(std::vector<PeptideHit>::iterator hit_it = pep_it->getHits().begin();
694 hit_it != pep_it->getHits().end(); ++hit_it )
696 std::vector<PeptideEvidence> evidences;
697 remove_copy_if(hit_it->getPeptideEvidences().begin(),
698 hit_it->getPeptideEvidences().end(),
699 back_inserter(evidences),
701 hit_it->setPeptideEvidences(evidences);
713 template <
class IdentificationType>
716 for (
typename std::vector<IdentificationType>::iterator it = ids.begin();
717 it != ids.end(); ++it)
724 static void removeUnreferencedProteins(
725 std::vector<ProteinIdentification>& proteins,
726 const std::vector<PeptideIdentification>& peptides);
735 static void updateProteinReferences(
736 std::vector<PeptideIdentification>& peptides,
737 const std::vector<ProteinIdentification>& proteins,
738 bool remove_peptides_without_reference =
false);
747 static void updateProteinReferences(
749 bool remove_peptides_without_reference =
false);
759 static bool updateProteinGroups(
760 std::vector<ProteinIdentification::ProteinGroup>& groups,
761 const std::vector<ProteinHit>& hits);
770 template <
class IdentificationType>
773 struct HasNoHits<IdentificationType> empty_filter;
774 removeMatchingItems(ids, empty_filter);
782 template <
class IdentificationType>
784 double threshold_score)
786 for (
typename std::vector<IdentificationType>::iterator id_it =
787 ids.begin(); id_it != ids.end(); ++id_it)
789 struct HasGoodScore<typename IdentificationType::HitType> score_filter(
790 threshold_score, id_it->isHigherScoreBetter());
791 keepMatchingItems(id_it->getHits(), score_filter);
800 template <class IdentificationType>
801 static void filterHitsByScore(IdentificationType& id,
802 double threshold_score)
804 struct HasGoodScore<typename IdentificationType::HitType> score_filter(
805 threshold_score, id->isHigherScoreBetter());
806 keepMatchingItems(id->getHits(), score_filter);
814 template <class IdentificationType>
815 static void keepNBestHits(std::vector<IdentificationType>& ids, Size n)
817 for (
typename std::vector<IdentificationType>::iterator id_it =
818 ids.begin(); id_it != ids.end(); ++id_it)
821 if (n < id_it->getHits().size()) id_it->getHits().resize(n);
839 template <
class IdentificationType>
846 struct HasMaxRank<typename IdentificationType::HitType>
847 rank_filter(min_rank - 1);
848 for (typename std::vector<IdentificationType>::iterator id_it =
849 ids.begin(); id_it != ids.end(); ++id_it)
851 removeMatchingItems(id_it->getHits(), rank_filter);
854 if (max_rank >= min_rank)
856 struct HasMaxRank<typename IdentificationType::HitType>
857 rank_filter(max_rank);
858 for (typename std::vector<IdentificationType>::iterator id_it =
859 ids.begin(); id_it != ids.end(); ++id_it)
861 keepMatchingItems(id_it->getHits(), rank_filter);
873 template <
class IdentificationType>
878 for (typename std::vector<IdentificationType>::iterator id_it =
879 ids.begin(); id_it != ids.end(); ++id_it)
881 removeMatchingItems(id_it->getHits(), decoy_filter);
892 template <
class IdentificationType>
894 const std::set<String> accessions)
897 for (auto& id_it : ids)
899 removeMatchingItems(id_it.getHits(), acc_filter);
910 template <
class IdentificationType>
912 const std::set<String>& accessions)
915 for (auto& id_it : ids)
917 keepMatchingItems(id_it.getHits(), acc_filter);
933 static void keepBestPeptideHits(
934 std::vector<PeptideIdentification>& peptides,
bool strict =
false);
944 static void filterPeptidesByLength(
945 std::vector<PeptideIdentification>& peptides,
Size min_length,
946 Size max_length = UINT_MAX);
956 static void filterPeptidesByCharge(
957 std::vector<PeptideIdentification>& peptides,
Int min_charge,
961 static void filterPeptidesByRT(std::vector<PeptideIdentification>& peptides,
962 double min_rt,
double max_rt);
965 static void filterPeptidesByMZ(std::vector<PeptideIdentification>& peptides,
966 double min_mz,
double max_mz);
979 static void filterPeptidesByMZError(
980 std::vector<PeptideIdentification>& peptides,
double mass_error,
990 template <
class Filter>
991 static void filterPeptideEvidences(
993 std::vector<PeptideIdentification>& peptides);
1006 static void filterPeptidesByRTPredictPValue(
1007 std::vector<PeptideIdentification>& peptides,
1008 const String& metavalue_key,
double threshold = 0.05);
1011 static void removePeptidesWithMatchingModifications(
1012 std::vector<PeptideIdentification>& peptides,
1013 const std::set<String>& modifications);
1016 static void keepPeptidesWithMatchingModifications(
1017 std::vector<PeptideIdentification>& peptides,
1018 const std::set<String>& modifications);
1027 static void removePeptidesWithMatchingSequences(
1028 std::vector<PeptideIdentification>& peptides,
1029 const std::vector<PeptideIdentification>& bad_peptides,
1030 bool ignore_mods =
false);
1039 static void keepPeptidesWithMatchingSequences(
1040 std::vector<PeptideIdentification>& peptides,
1041 const std::vector<PeptideIdentification>& good_peptides,
1042 bool ignore_mods =
false);
1045 static void keepUniquePeptidesPerProtein(std::vector<PeptideIdentification>&
1053 static void removeDuplicatePeptideHits(std::vector<PeptideIdentification>&
1054 peptides,
bool seq_only =
false);
1064 double peptide_threshold_score,
1065 double protein_threshold_score)
1069 protein_threshold_score);
1075 exp_it != experiment.
end(); ++exp_it)
1077 filterHitsByScore(exp_it->getPeptideIdentifications(),
1078 peptide_threshold_score);
1079 removeEmptyIdentifications(exp_it->getPeptideIdentifications());
1080 updateProteinReferences(exp_it->getPeptideIdentifications(),
1091 std::vector<PeptideIdentification> all_peptides;
1095 exp_it != experiment.
end(); ++exp_it)
1097 std::vector<PeptideIdentification>& peptides =
1098 exp_it->getPeptideIdentifications();
1099 keepNBestHits(peptides, n);
1100 removeEmptyIdentifications(peptides);
1101 updateProteinReferences(peptides,
1103 all_peptides.insert(all_peptides.end(), peptides.begin(),
1112 template <
class MapType>
1117 for (
auto& feat : map)
1119 keepNBestHits(feat.getPeptideIdentifications(), n);
1121 keepNBestHits(map.getUnassignedPeptideIdentifications(), n);
1124 template <
class MapType>
1131 static void keepBestPerPeptide(std::vector<PeptideIdentification>& pep_ids,
bool ignore_mods,
bool ignore_charges,
Size nr_best_spectrum)
1133 annotateBestPerPeptide(pep_ids, ignore_mods, ignore_charges, nr_best_spectrum);
1135 keepMatchingItemsUnroll(pep_ids, best_per_peptide);
1138 static void keepBestPerPeptidePerRun(std::vector<ProteinIdentification>& prot_ids, std::vector<PeptideIdentification>& pep_ids,
bool ignore_mods,
bool ignore_charges,
Size nr_best_spectrum)
1140 annotateBestPerPeptidePerRun(prot_ids, pep_ids, ignore_mods, ignore_charges, nr_best_spectrum);
1142 keepMatchingItemsUnroll(pep_ids, best_per_peptide);
1145 template <
class MapType>
1150 RunToSequenceToChargeToPepHitP best_peps_per_run;
1151 for (
const auto& idrun : prot_ids)
1153 best_peps_per_run[idrun.getIdentifier()] = SequenceToChargeToPepHitP();
1156 for (
auto& feat : prot_and_pep_ids)
1158 annotateBestPerPeptidePerRunWithData(best_peps_per_run, feat.getPeptideIdentifications(), ignore_mods, ignore_charges, nr_best_spectrum);
1161 annotateBestPerPeptidePerRunWithData(best_peps_per_run, prot_and_pep_ids.getUnassignedPeptideIdentifications(), ignore_mods, ignore_charges, nr_best_spectrum);
1164 keepMatchingPeptideHits(prot_and_pep_ids, best_per_peptide);
1169 static void annotateBestPerPeptidePerRun(
const std::vector<ProteinIdentification>& prot_ids, std::vector<PeptideIdentification>& pep_ids,
bool ignore_mods,
bool ignore_charges,
Size nr_best_spectrum)
1171 RunToSequenceToChargeToPepHitP best_peps_per_run;
1172 for (
const auto&
id : prot_ids)
1174 best_peps_per_run[
id.getIdentifier()] = SequenceToChargeToPepHitP();
1176 annotateBestPerPeptidePerRunWithData(best_peps_per_run, pep_ids, ignore_mods, ignore_charges, nr_best_spectrum);
1184 for (
auto &pep : pep_ids)
1186 SequenceToChargeToPepHitP& best_pep = best_peps_per_run[pep.getIdentifier()];
1187 annotateBestPerPeptideWithData(best_pep, pep, ignore_mods, ignore_charges, nr_best_spectrum);
1196 SequenceToChargeToPepHitP best_pep;
1197 for (
auto& pep : pep_ids)
1199 annotateBestPerPeptideWithData(best_pep, pep, ignore_mods, ignore_charges, nr_best_spectrum);
1213 auto pepIt = pep.
getHits().begin();
1214 auto pepItEnd = nr_best_spectrum == 0 || pep.
getHits().size() <= nr_best_spectrum ? pep.
getHits().end() : pep.
getHits().begin() + nr_best_spectrum;
1215 for (; pepIt != pepItEnd; ++pepIt)
1229 int lookup_charge = 0;
1230 if (!ignore_charges)
1236 auto it_inserted = best_pep.emplace(std::move(lookup_seq), ChargeToPepHitP());
1237 auto it_inserted_chg = it_inserted.first->second.emplace(lookup_charge, &hit);
1239 PeptideHit* &p = it_inserted_chg.first->second;
1240 if (!it_inserted_chg.second)
1267 const std::vector<FASTAFile::FASTAEntry>& proteins)
1269 std::set<String> accessions;
1270 for (std::vector<FASTAFile::FASTAEntry>::const_iterator it =
1271 proteins.begin(); it != proteins.end(); ++it)
1273 accessions.insert(it->identifier);
1283 exp_it != experiment.
end(); ++exp_it)
1285 if (exp_it->getMSLevel() == 2)
1287 keepHitsMatchingProteins(exp_it->getPeptideIdentifications(),
1289 removeEmptyIdentifications(exp_it->getPeptideIdentifications());
1290 updateHitRanks(exp_it->getPeptideIdentifications());
1300 static void keepBestMatchPerQuery(
1304 static void filterQueryMatchesByScore(
HasMetaValue(const String &key_, const DataValue &value_)
Definition: IDFilter.h:168
Is the score of this hit at least as good as the given value?
Definition: IDFilter.h:101
HasMaxMetaValue(const String &key_, const double &value_)
Definition: IDFilter.h:191
Int getEnd() const
get the position of the last AA of the peptide in protein coordinates (starting at 0 for the N-termin...
bool operator()(const PeptideEvidence &evidence) const
Definition: IDFilter.h:291
bool higher_score_better
Definition: IDFilter.h:106
void setMetaValue(const String &name, const DataValue &value)
Sets the DataValue corresponding to a name.
Filter Peptide Hit by its digestion product.
Definition: IDFilter.h:387
Given a list of protein accessions, do any occur in the annotation(s) of this hit?
Definition: IDFilter.h:231
String identifier
Definition: FASTAFile.h:78
Int getCharge() const
returns the charge of the peptide
ItemMap items
Definition: IDFilter.h:307
PeptideDigestionFilter(EnzymaticDigestion &digestion, Int min, Int max)
Definition: IDFilter.h:396
ProteaseDigestion & digestion_
Definition: IDFilter.h:439
bool operator()(const IdentificationType &id) const
Definition: IDFilter.h:501
bool isEmpty() const
Test if the value is empty.
Definition: DataValue.h:375
static void keepHitsMatchingProteins(std::vector< IdentificationType > &ids, const std::set< String > &accessions)
Filters peptide or protein identifications according to the given proteins (positive).
Definition: IDFilter.h:911
GetMatchingItems(std::vector< Entry > &records)
Definition: IDFilter.h:309
static void removeMatchingItemsUnroll(IDContainer &items, const Predicate &pred)
Remove Hit items that satisfy a condition in one of our ID containers (e.g. vector of Peptide or Prot...
Definition: IDFilter.h:547
static void annotateBestPerPeptidePerRun(const std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)
Definition: IDFilter.h:1169
static void keepMatchingItemsUnroll(IDContainer &items, const Predicate &pred)
Keep Hit items that satisfy a condition in one of our ID containers (e.g. vector of Peptide or Protei...
Definition: IDFilter.h:557
static void keepMatchingPeptideHits(MapType &prot_and_pep_ids, Predicate &pred)
Definition: IDFilter.h:566
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
static void filterHitsByRank(std::vector< IdentificationType > &ids, Size min_rank, Size max_rank)
Filters peptide or protein identifications according to the ranking of the hits.
Definition: IDFilter.h:840
Iterator end()
Definition: MSExperiment.h:167
Iterator begin()
Definition: MSExperiment.h:157
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
Is peptide evidence digestion product of some protein.
Definition: IDFilter.h:433
double score
Definition: IDFilter.h:105
static void filterHitsByScore(std::vector< IdentificationType > &ids, double threshold_score)
Filters peptide or protein identifications according to the score of the hits.
Definition: IDFilter.h:783
std::unordered_map< std::string, ChargeToPepHitP > SequenceToChargeToPepHitP
Definition: IDFilter.h:89
const std::vector< ProteinIdentification > & getProteinIdentifications() const
returns a const reference to the protein ProteinIdentification vector
bool operator()(const HitType &hit) const
Definition: IDFilter.h:113
double getScore() const
returns the PSM score
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:43
std::set< String > extractProteinAccessionsSet() const
extracts the set of non-empty protein accessions from peptide evidences
Representation of a peptide evidence.
Definition: PeptideEvidence.h:50
static void filterHitsByScore(PeakMap &experiment, double peptide_threshold_score, double protein_threshold_score)
Filters an MS/MS experiment according to score thresholds.
Definition: IDFilter.h:1063
void filterPeptideEvidences(std::vector< PeptideIdentification > &peptides)
Definition: IDFilter.h:482
static void removeDecoyHits(std::vector< IdentificationType > &ids)
Removes hits annotated as decoys from peptide or protein identifications.
Definition: IDFilter.h:874
const String & getHitKey(const PeptideEvidence &p) const
Definition: IDFilter.h:330
HasMatchingAccessionUnordered(const std::unordered_set< String > &accessions_)
Definition: IDFilter.h:237
static void keepNBestHits(PeakMap &experiment, Size n)
Filters an MS/MS experiment by keeping the N best peptide hits for every spectrum.
Definition: IDFilter.h:1087
std::map< Int, PeptideHit * > ChargeToPepHitP
Typedefs.
Definition: IDFilter.h:88
bool operator()(const PeptideEvidence &evidence) const
Definition: IDFilter.h:255
static void keepMatchingItems(Container &items, const Predicate &pred)
Keep items that satisfy a condition in a container (e.g. vector), removing all others.
Definition: IDFilter.h:539
std::vector< SpectrumType >::iterator Iterator
Mutable iterator.
Definition: MSExperiment.h:111
bool isHigherScoreBetter() const
returns the peptide score orientation
const String & getProteinAccession() const
get the protein accession the peptide matches to. If not available the empty string is returned...
double value
Definition: IDFilter.h:189
static void annotateBestPerPeptidePerRunWithData(RunToSequenceToChargeToPepHitP &best_peps_per_run, std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)
Definition: IDFilter.h:1182
GetMatchingItems()
Definition: IDFilter.h:318
const std::set< String > & accessions
Definition: IDFilter.h:271
Representation of a protein hit.
Definition: ProteinHit.h:57
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
static AASequence fromString(const String &s, bool permissive=true)
create AASequence object by parsing an OpenMS string
bool operator()(const HitType &hit) const
Definition: IDFilter.h:173
String key
Definition: IDFilter.h:165
static void annotateBestPerPeptide(std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)
Definition: IDFilter.h:1194
Int getStart() const
get the position in the protein (starting at 0 for the N-terminus). If not available UNKNOWN_POSITION...
Class for the enzymatic digestion of proteins.
Definition: ProteaseDigestion.h:60
Class for the enzymatic digestion of sequences.
Definition: EnzymaticDigestion.h:62
Exception indicating that an invalid parameter was handed over to an algorithm.
Definition: Exception.h:347
Is a meta value with given key and value set on this hit?
Definition: IDFilter.h:161
std::map< std::string, SequenceToChargeToPepHitP > RunToSequenceToChargeToPepHitP
Definition: IDFilter.h:90
void sort()
Sorts the hits by score.
static void FilterPeptideEvidences(EvidenceFilter &filter, std::vector< PeptideIdentification > &peptides)
remove peptide evidences based on a filter
Definition: IDFilter.h:686
#define OPENMS_LOG_WARN
Macro if a warning, a piece of information which should be read by the user, should be logged...
Definition: LogStream.h:460
const std::vector< PeptideHit > & getHits() const
returns the peptide hits as const
Collection of functions for filtering peptide and protein identifications.
Definition: IDFilter.h:77
const String & getAccession() const
returns the accession of the protein
bool operator()(PeptideHit &p)
Definition: IDFilter.h:404
DataValue value
Definition: IDFilter.h:166
HitType argument_type
Definition: IDFilter.h:103
bool operator()(const HitType &hit) const
Definition: IDFilter.h:196
static void annotateBestPerPeptideWithData(SequenceToChargeToPepHitP &best_pep, PeptideIdentification &pep, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)
Definition: IDFilter.h:1207
static void removeHitsMatchingProteins(std::vector< IdentificationType > &ids, const std::set< String > accessions)
Filters peptide or protein identifications according to the given proteins (negative).
Definition: IDFilter.h:893
bool filterByMissedCleavages(const String &sequence, std::function< bool(const Int)> filter) const
Filter based on the number of missed cleavages.
HasDecoyAnnotation()
Definition: IDFilter.h:212
std::map< String, Entry * > ItemMap
Definition: IDFilter.h:306
DigestionFilter(std::vector< FASTAFile::FASTAEntry > &entries, ProteaseDigestion &digestion, bool ignore_missed_cleavages, bool methionine_cleavage)
Definition: IDFilter.h:443
Builds a map index of data that have a String index to find matches and return the objects...
Definition: IDFilter.h:303
static bool getBestHit(const std::vector< IdentificationType > &identifications, bool assume_sorted, typename IdentificationType::HitType &best_hit)
Finds the best-scoring hit in a vector of peptide or protein identifications.
Definition: IDFilter.h:617
static void keepBestPerPeptide(std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)
Filters PeptideHits from PeptideIdentification by keeping only the best peptide hits for every peptid...
Definition: IDFilter.h:1131
GetMatchingItems< PeptideEvidence, FASTAFile::FASTAEntry > accession_resolver_
Definition: IDFilter.h:438
String toString() const
returns the peptide as string with modifications embedded in brackets
static Size countHits(const std::vector< IdentificationType > &ids)
Returns the total number of peptide/protein hits in a vector of peptide/protein identifications.
Definition: IDFilter.h:593
Is this a decoy hit?
Definition: IDFilter.h:206
HasGoodScore(double score_, bool higher_score_better_)
Definition: IDFilter.h:108
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:89
bool hasValidLimits() const
start and end numbers in evidence represent actual numeric indices
HitType argument_type
Definition: IDFilter.h:208
static Int disabledValue()
Definition: IDFilter.h:400
HitType argument_type
Definition: IDFilter.h:186
Int min_cleavages_
Definition: IDFilter.h:391
HitType argument_type
Definition: IDFilter.h:233
Is the list of hits of this peptide/protein ID empty?
Definition: IDFilter.h:497
bool ignore_missed_cleavages_
Definition: IDFilter.h:440
void filterPeptideSequences(std::vector< PeptideHit > &hits)
Definition: IDFilter.h:419
const Entry & getValue(const PeptideEvidence &evidence) const
Definition: IDFilter.h:335
static void keepHitsMatchingProteins(PeakMap &experiment, const std::vector< FASTAFile::FASTAEntry > &proteins)
Filters an MS/MS experiment according to the given proteins.
Definition: IDFilter.h:1265
bool operator()(const PeptideEvidence &evidence) const
Definition: IDFilter.h:453
static void keepBestPerPeptidePerRun(MapType &prot_and_pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)
Definition: IDFilter.h:1146
const AASequence & getSequence() const
returns the peptide sequence without trailing or following spaces
static void removeEmptyIdentifications(std::vector< IdentificationType > &ids)
Removes peptide or protein identifications that have no hits in them.
Definition: IDFilter.h:771
bool methionine_cleavage_
Definition: IDFilter.h:441
EnzymaticDigestion & digestion_
Definition: IDFilter.h:390
Representation of a peptide hit.
Definition: PeptideHit.h:54
bool operator()(const HitType &hit) const
Definition: IDFilter.h:144
Not all required information provided.
Definition: Exception.h:195
static void keepBestPerPeptidePerRun(std::vector< ProteinIdentification > &prot_ids, std::vector< PeptideIdentification > &pep_ids, bool ignore_mods, bool ignore_charges, Size nr_best_spectrum)
Definition: IDFilter.h:1138
PeptideEvidence argument_type
Definition: IDFilter.h:435
HitType argument_type
Definition: IDFilter.h:163
HasMaxRank(Size rank_)
Definition: IDFilter.h:135
A more convenient string class.
Definition: String.h:58
HasMatchingAccession(const std::set< String > &accessions_)
Definition: IDFilter.h:273
Class to hold strings, numeric values, lists of strings and lists of numeric values.
Definition: DataValue.h:56
FASTA entry type (identifier, description and sequence)
Definition: FASTAFile.h:76
const std::unordered_set< String > & accessions
Definition: IDFilter.h:235
A container for consensus elements.
Definition: ConsensusMap.h:79
String toUnmodifiedString() const
returns the peptide as string without any modifications or (e.g., "PEPTIDER")
static void keepNBestPeptideHits(MapType &map, Size n)
Filters a Consensus/FeatureMap by keeping the N best peptide hits for every spectrum.
Definition: IDFilter.h:1113
Invalid value exception.
Definition: Exception.h:335
static void updateHitRanks(std::vector< IdentificationType > &ids)
Updates the hit ranks on all peptide or protein IDs.
Definition: IDFilter.h:714
Is the rank of this hit below or at the given cut-off?
Definition: IDFilter.h:129
IdentificationType argument_type
Definition: IDFilter.h:499
PeptideHit argument_type
Definition: IDFilter.h:395
HitType argument_type
Definition: IDFilter.h:131
A method or algorithm argument contains illegal values.
Definition: Exception.h:648
static void removeMatchingPeptideHits(MapType &prot_and_pep_ids, Predicate &pred)
Definition: IDFilter.h:576
Size rank
Definition: IDFilter.h:133
HitType argument_type
Definition: IDFilter.h:305
String key
Definition: IDFilter.h:188
const String & getKey(const FASTAFile::FASTAEntry &entry) const
Definition: IDFilter.h:320
bool isValidProduct(const String &protein, int pep_pos, int pep_length, bool ignore_missed_cleavages=true, bool allow_nterm_protein_cleavage=false, bool allow_random_asp_pro_cleavage=false) const
Variant of EnzymaticDigestion::isValidProduct() with support for n-term protein cleavage and random D...
static void removeMatchingItems(Container &items, const Predicate &pred)
Remove items that satisfy a condition from a container (e.g. vector)
Definition: IDFilter.h:531
bool operator()(const PeptideHit &hit) const
Definition: IDFilter.h:277
bool operator()(const PeptideHit &hit) const
Definition: IDFilter.h:241
static void removeEmptyIdentifications(MapType &prot_and_pep_ids)
Definition: IDFilter.h:1125
bool operator()(const HitType &hit) const
Definition: IDFilter.h:216
Given a list of protein accessions, do any occur in the annotation(s) of this hit?
Definition: IDFilter.h:267
bool operator()(const ProteinHit &hit) const
Definition: IDFilter.h:250
Int max_cleavages_
Definition: IDFilter.h:392
bool exists(const HitType &hit) const
Definition: IDFilter.h:325
HitType argument_type
Definition: IDFilter.h:269
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
bool operator()(const ProteinHit &hit) const
Definition: IDFilter.h:286
Does a meta value of this hit have at most the given value?
Definition: IDFilter.h:184