| OpenMS 2.5.0

IdentifiedSequence.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CHEMISTRY/AASequence.h>
38 #include <OpenMS/CHEMISTRY/NASequence.h>
39 #include <OpenMS/METADATA/ID/MoleculeParentMatch.h>
40 #include <OpenMS/METADATA/ID/ScoredProcessingResult.h>
41
42 #include <boost/multi_index_container.hpp>
43 #include <boost/multi_index/ordered_index.hpp>
44 #include <boost/multi_index/member.hpp>
45
46 namespace OpenMS
47 {
48 namespace IdentificationDataInternal
49 {
51 template <typename SeqType>
52 struct IdentifiedSequence: public ScoredProcessingResult
53 {
54 SeqType sequence;
55
56 ParentMatches parent_matches;
57
58 explicit IdentifiedSequence(
59 const SeqType& sequence,
60 const ParentMatches& parent_matches = ParentMatches(),
61 const AppliedProcessingSteps& steps_and_scores =
62 AppliedProcessingSteps()):
63 ScoredProcessingResult(steps_and_scores), sequence(sequence),
64 parent_matches(parent_matches)
65 {
66 }
67
68 IdentifiedSequence(const IdentifiedSequence& other) = default;
69
70 IdentifiedSequence& operator+=(const IdentifiedSequence& other)
71 {
72 ScoredProcessingResult::operator+=(other);
73 // merge parent matches:
74 for (const auto& pair : other.parent_matches)
75 {
76 auto pos = parent_matches.find(pair.first);
77 if (pos == parent_matches.end()) // new entry
78 {
79 parent_matches.insert(pair);
80 }
81 else // merge entries
82 {
83 pos->second.insert(pair.second.begin(), pair.second.end());
84 }
85 }
86
87 return *this;
88 }
89
90 bool allParentsAreDecoys() const
91 {
92 if (parent_matches.empty())
93 {
94 String msg = "no parent found for identified molecule";
95 throw Exception::MissingInformation(__FILE__, __LINE__,
96 OPENMS_PRETTY_FUNCTION, msg);
97 }
98 for (const auto& pair : parent_matches)
99 {
100 if (!pair.first->is_decoy) return false;
101 }
102 return true;
103 }
104 };
105
106 typedef IdentifiedSequence<AASequence> IdentifiedPeptide;
107 typedef IdentifiedSequence<NASequence> IdentifiedOligo;
108
109 // identified peptides indexed by their sequences:
110 typedef boost::multi_index_container<
111 IdentifiedPeptide,
112 boost::multi_index::indexed_by<
113 boost::multi_index::ordered_unique<boost::multi_index::member<
114 IdentifiedPeptide, AASequence, &IdentifiedPeptide::sequence>>>
115 > IdentifiedPeptides;
116 typedef IteratorWrapper<IdentifiedPeptides::iterator> IdentifiedPeptideRef;
117
118 // identified oligos indexed by their sequences:
119 typedef boost::multi_index_container<
120 IdentifiedOligo,
121 boost::multi_index::indexed_by<
122 boost::multi_index::ordered_unique<boost::multi_index::member<
123 IdentifiedOligo, NASequence, &IdentifiedOligo::sequence>>>
124 > IdentifiedOligos;
125 typedef IteratorWrapper<IdentifiedOligos::iterator> IdentifiedOligoRef;
126
127 }
128 }
OpenMS::IdentificationDataInternal::IdentifiedPeptideRef
IteratorWrapper< IdentifiedPeptides::iterator > IdentifiedPeptideRef
Definition: IdentifiedSequence.h:116
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::IdentificationDataInternal::IdentifiedSequence::operator+=
IdentifiedSequence & operator+=(const IdentifiedSequence &other)
Definition: IdentifiedSequence.h:70
ScoredProcessingResult.h
OpenMS::IdentificationDataInternal::IdentifiedOligo
IdentifiedSequence< NASequence > IdentifiedOligo
Definition: IdentifiedSequence.h:107
AASequence.h
OpenMS::IdentificationDataInternal::IdentifiedSequence::sequence
SeqType sequence
Definition: IdentifiedSequence.h:54
NASequence.h
OpenMS::IdentificationDataInternal::IteratorWrapper
Wrapper that adds operator< to iterators, so they can be used as (part of) keys in maps/sets or multi...
Definition: MetaData.h:43
OpenMS::IdentificationDataInternal::IdentifiedSequence::IdentifiedSequence
IdentifiedSequence(const SeqType &sequence, const ParentMatches &parent_matches=ParentMatches(), const AppliedProcessingSteps &steps_and_scores=AppliedProcessingSteps())
Definition: IdentifiedSequence.h:58
MoleculeParentMatch.h
OpenMS::IdentificationDataInternal::IdentifiedSequence::parent_matches
ParentMatches parent_matches
Definition: IdentifiedSequence.h:56
OpenMS::IdentificationDataInternal::IdentifiedSequence
Identified sequence (peptide or oligonucleotide)
Definition: IdentifiedSequence.h:52
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:113
OpenMS::IdentificationDataInternal::AppliedProcessingSteps
boost::multi_index_container< AppliedProcessingStep, boost::multi_index::indexed_by< boost::multi_index::sequenced<>, boost::multi_index::ordered_unique< boost::multi_index::member< AppliedProcessingStep, boost::optional< ProcessingStepRef >, &AppliedProcessingStep::processing_step_opt > > > > AppliedProcessingSteps
Definition: AppliedProcessingStep.h:116
OpenMS::IdentificationDataInternal::IdentifiedOligoRef
IteratorWrapper< IdentifiedOligos::iterator > IdentifiedOligoRef
Definition: IdentifiedSequence.h:125
OpenMS::IdentificationDataInternal::IdentifiedOligos
boost::multi_index_container< IdentifiedOligo, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< IdentifiedOligo, NASequence, &IdentifiedOligo::sequence > > > > IdentifiedOligos
Definition: IdentifiedSequence.h:124
OpenMS::IdentificationDataInternal::ParentMatches
std::map< ParentMoleculeRef, std::set< MoleculeParentMatch > > ParentMatches
mapping: parent molecule -> match information
Definition: MoleculeParentMatch.h:101
OpenMS::IdentificationDataInternal::ScoredProcessingResult
Base class for ID data with scores and processing steps (and meta info)
Definition: ScoredProcessingResult.h:44
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:195
OpenMS::IdentificationDataInternal::ScoredProcessingResult::steps_and_scores
AppliedProcessingSteps steps_and_scores
Definition: ScoredProcessingResult.h:46
OpenMS::IdentificationDataInternal::IdentifiedPeptide
IdentifiedSequence< AASequence > IdentifiedPeptide
Definition: IdentifiedSequence.h:106
OpenMS::IdentificationDataInternal::ScoredProcessingResult::operator+=
ScoredProcessingResult & operator+=(const ScoredProcessingResult &other)
Merge in data from another object.
Definition: ScoredProcessingResult.h:107
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:62
OpenMS::IdentificationDataInternal::IdentifiedPeptides
boost::multi_index_container< IdentifiedPeptide, boost::multi_index::indexed_by< boost::multi_index::ordered_unique< boost::multi_index::member< IdentifiedPeptide, AASequence, &IdentifiedPeptide::sequence > > > > IdentifiedPeptides
Definition: IdentifiedSequence.h:115
OpenMS::IdentificationDataInternal::IdentifiedSequence::allParentsAreDecoys
bool allParentsAreDecoys() const
Definition: IdentifiedSequence.h:90