OpenMS  3.0.0
IdentifiedSequence.h
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31 // $Maintainer: Hendrik Weisser $
32 // $Authors: Hendrik Weisser $
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34 
35 #pragma once
36 
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>
53  {
54  SeqType sequence;
55 
57 
59  const SeqType& sequence,
65  {
66  }
67 
68  IdentifiedSequence(const IdentifiedSequence& other) = default;
69 
71  {
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 
108 
109  // identified peptides indexed by their sequences:
110  typedef boost::multi_index_container<
112  boost::multi_index::indexed_by<
113  boost::multi_index::ordered_unique<boost::multi_index::member<
117 
118  // identified oligos indexed by their sequences:
119  typedef boost::multi_index_container<
121  boost::multi_index::indexed_by<
122  boost::multi_index::ordered_unique<boost::multi_index::member<
126 
127  }
128 }
OpenMS::IdentificationDataInternal::IdentifiedOligo
IdentifiedSequence< NASequence > IdentifiedOligo
Definition: IdentifiedSequence.h:107
OpenMS::IdentificationDataInternal::IdentifiedSequence::merge
IdentifiedSequence & merge(const IdentifiedSequence &other)
Definition: IdentifiedSequence.h:70
OpenMS::IdentificationDataInternal::IdentifiedPeptide
IdentifiedSequence< AASequence > IdentifiedPeptide
Definition: IdentifiedSequence.h:106
OpenMS::NASequence
Representation of a nucleic acid sequence.
Definition: NASequence.h:61
ParentMatch.h
OpenMS::String
A more convenient string class.
Definition: String.h:58
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::ScoredProcessingResult::steps_and_scores
AppliedProcessingSteps steps_and_scores
Definition: ScoredProcessingResult.h:46
OpenMS::IdentificationDataInternal::ParentMatches
std::map< ParentSequenceRef, std::set< ParentMatch > > ParentMatches
mapping: parent sequence -> match information
Definition: ParentMatch.h:101
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, std::optional< ProcessingStepRef >, &AppliedProcessingStep::processing_step_opt > > > > AppliedProcessingSteps
Definition: AppliedProcessingStep.h:133
NASequence.h
OpenMS::IdentificationDataInternal::IdentifiedSequence::parent_matches
ParentMatches parent_matches
Definition: IdentifiedSequence.h:56
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::IdentificationDataInternal::IdentifiedOligoRef
IteratorWrapper< IdentifiedOligos::iterator > IdentifiedOligoRef
Definition: IdentifiedSequence.h:125
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:45
OpenMS::IdentificationDataInternal::IdentifiedSequence::sequence
SeqType sequence
Definition: IdentifiedSequence.h:54
ScoredProcessingResult.h
AASequence.h
OpenMS::IdentificationDataInternal::ScoredProcessingResult
Base class for ID data with scores and processing steps (and meta info)
Definition: ScoredProcessingResult.h:44
OpenMS::IdentificationDataInternal::IdentifiedSequence
Representation of an identified sequence (peptide or oligonucleotide)
Definition: IdentifiedSequence.h:52
OpenMS::AASequence
Representation of a peptide/protein sequence.
Definition: AASequence.h:111
OpenMS::Exception::MissingInformation
Not all required information provided.
Definition: Exception.h:186
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
OpenMS::IdentificationDataInternal::IdentifiedPeptideRef
IteratorWrapper< IdentifiedPeptides::iterator > IdentifiedPeptideRef
Definition: IdentifiedSequence.h:116
OpenMS::IdentificationDataInternal::IdentifiedSequence::IdentifiedSequence
IdentifiedSequence(const SeqType &sequence, const ParentMatches &parent_matches=ParentMatches(), const AppliedProcessingSteps &steps_and_scores=AppliedProcessingSteps())
Definition: IdentifiedSequence.h:58
OpenMS::IdentificationDataInternal::ScoredProcessingResult::merge
ScoredProcessingResult & merge(const ScoredProcessingResult &other)
Merge in data from another object.
Definition: ScoredProcessingResult.h:107