| OpenMS 2.5.0

ConsensusMapMergerAlgorithm.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Julianus Pfeuffer $
32 // $Authors: Julianus Pfeuffer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
38 #include <OpenMS/CONCEPT/Exception.h>
39 #include <OpenMS/CONCEPT/ProgressLogger.h>
40 #include <OpenMS/KERNEL/ConsensusMap.h>
41 #include <OpenMS/METADATA/ExperimentalDesign.h>
42
43 #include <unordered_set>
44
45 namespace OpenMS
46 {
63 class OPENMS_DLLAPI ConsensusMapMergerAlgorithm:
64 public DefaultParamHandler,
65 public ProgressLogger
66 {
67 public:
68 ConsensusMapMergerAlgorithm ();
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;
103 bool checkRunSettings_(const ProteinIdentification& idRun, const ProteinIdentification& ref, const String& experiment_type) const;
104
105
106 static size_t accessionHash_(const ProteinHit& p)
107 {
108 return std::hash<String>()(p.getAccession());
109 }
110 static bool accessionEqual_(const ProteinHit& p1, const ProteinHit& p2)
111 {
112 return p1.getAccession() == p2.getAccession();
113 }
114 using hash_type = std::size_t (*)(const ProteinHit&);
115 using equal_type = bool (*)(const ProteinHit&, const ProteinHit&);
116
117 };
118 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::ConsensusMapMergerAlgorithm::hash_type
std::size_t(*)(const ProteinHit &) hash_type
Definition: ConsensusMapMergerAlgorithm.h:114
OpenMS::ProteinHit::getAccession
const String & getAccession() const
returns the accession of the protein
OpenMS::ConsensusMapMergerAlgorithm::accessionHash_
static size_t accessionHash_(const ProteinHit &p)
Definition: ConsensusMapMergerAlgorithm.h:106
Exception.h
OpenMS::ProteinHit
Representation of a protein hit.
Definition: ProteinHit.h:57
ExperimentalDesign.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::ConsensusMapMergerAlgorithm
Merges identification data in ConsensusMaps.
Definition: ConsensusMapMergerAlgorithm.h:63
ConsensusMap.h
OpenMS::ConsensusMapMergerAlgorithm::accessionEqual_
static bool accessionEqual_(const ProteinHit &p1, const ProteinHit &p2)
Definition: ConsensusMapMergerAlgorithm.h:110
ProgressLogger.h
OpenMS::ExperimentalDesign
Representation of the Experimental Design in OpenMS. Instances can be loaded via the ExperimentalDesi...
Definition: ExperimentalDesign.h:85
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
OpenMS::ConsensusMapMergerAlgorithm::equal_type
bool(*)(const ProteinHit &, const ProteinHit &) equal_type
Definition: ConsensusMapMergerAlgorithm.h:115
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79