| OpenMS 2.5.0

BasicProteinInferenceAlgorithm.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 #pragma once
35
36 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
37 #include <OpenMS/CONCEPT/ProgressLogger.h>
38 #include <OpenMS/METADATA/ProteinIdentification.h>
39 #include <OpenMS/METADATA/PeptideHit.h>
40
41 namespace OpenMS
42 {
58 class OPENMS_DLLAPI BasicProteinInferenceAlgorithm :
59 public DefaultParamHandler,
60 public ProgressLogger
61 {
62 public:
63
67 enum class AggregationMethod
68 {
69 PROD,
70 SUM,
71 MAXIMUM
72 };
73
75 BasicProteinInferenceAlgorithm();
76
80 void run(std::vector<PeptideIdentification> &pep_ids, std::vector<ProteinIdentification> &prot_ids) const;
81 void run(std::vector<PeptideIdentification> &pep_ids, ProteinIdentification &prot_id) const;
82
83 private:
84
94 void processRun_(
95 std::unordered_map<std::string, std::pair<ProteinHit*, Size>>& acc_to_protein_hitP_and_count,
96 std::unordered_map<std::string, std::map<Int, PeptideHit*>>& best_pep,
97 ProteinIdentification& prot_run,
98 std::vector<PeptideIdentification>& pep_ids,
99 Size min_peptides_per_protein) const;
100 };
101 } //namespace OpenMS
ProteinIdentification.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::BasicProteinInferenceAlgorithm::AggregationMethod
AggregationMethod
The aggregation method.
Definition: BasicProteinInferenceAlgorithm.h:67
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::IntensityAveragingMethod::SUM
PeptideHit.h
ProgressLogger.h
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
OpenMS::BasicProteinInferenceAlgorithm
Algorithm class that implements simple protein inference by aggregation of peptide scores...
Definition: BasicProteinInferenceAlgorithm.h:58
DefaultParamHandler.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127