OpenMS  3.0.0
ConsensusMapMergerAlgorithm.h
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31 // $Maintainer: Julianus Pfeuffer $
32 // $Authors: Julianus Pfeuffer $
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34 
35 #pragma once
36 
42 
43 #include <unordered_set>
44 
45 namespace OpenMS
46 {
63  class OPENMS_DLLAPI ConsensusMapMergerAlgorithm:
64  public DefaultParamHandler,
65  public ProgressLogger
66  {
67  public:
69 
78  void mergeProteinsAcrossFractionsAndReplicates(ConsensusMap& cmap, const ExperimentalDesign& exp_design) const;
79 
84  void mergeAllIDRuns(ConsensusMap& cmap) const;
85 
90  void mergeProteinIDRuns(ConsensusMap &cmap,
91  const std::map<unsigned, unsigned>& mapIdx_to_new_protIDRun) const;
92 
93  private:
94 
99  bool checkOldRunConsistency_(const std::vector<ProteinIdentification>& protRuns, const String& experiment_type) const;
101  bool checkOldRunConsistency_(const std::vector<ProteinIdentification>& protRuns, const ProteinIdentification& ref, const String& experiment_type) const;
102 
103 
104  static size_t accessionHash_(const ProteinHit& p)
105  {
106  return std::hash<String>()(p.getAccession());
107  }
108  static bool accessionEqual_(const ProteinHit& p1, const ProteinHit& p2)
109  {
110  return p1.getAccession() == p2.getAccession();
111  }
112  using hash_type = std::size_t (*)(const ProteinHit&);
113  using equal_type = bool (*)(const ProteinHit&, const ProteinHit&);
114 
115  };
116 } // namespace OpenMS
DefaultParamHandler.h
OpenMS::ExperimentalDesign
Representation of an experimental design in OpenMS. Instances can be loaded with the ExperimentalDesi...
Definition: ExperimentalDesign.h:242
OpenMS::ConsensusMapMergerAlgorithm::hash_type
std::size_t(*)(const ProteinHit &) hash_type
Definition: ConsensusMapMergerAlgorithm.h:112
OpenMS::String
A more convenient string class.
Definition: String.h:58
ConsensusMap.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:58
OpenMS::ConsensusMapMergerAlgorithm::equal_type
bool(*)(const ProteinHit &, const ProteinHit &) equal_type
Definition: ConsensusMapMergerAlgorithm.h:113
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:70
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS::ProteinHit::getAccession
const String & getAccession() const
returns the accession of the protein
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
Exception.h
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
OpenMS::ConsensusMapMergerAlgorithm
Merges identification data in ConsensusMaps.
Definition: ConsensusMapMergerAlgorithm.h:63
ProgressLogger.h
OpenMS::ConsensusMapMergerAlgorithm::accessionEqual_
static bool accessionEqual_(const ProteinHit &p1, const ProteinHit &p2)
Definition: ConsensusMapMergerAlgorithm.h:108
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
ExperimentalDesign.h
OpenMS::ConsensusMapMergerAlgorithm::accessionHash_
static size_t accessionHash_(const ProteinHit &p)
Definition: ConsensusMapMergerAlgorithm.h:104