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BayesianProteinInferenceAlgorithm.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 //#define INFERENCE_BENCH
37
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/METADATA/ExperimentalDesign.h>
40 #include <OpenMS/CONCEPT/ProgressLogger.h>
41 #include <OpenMS/MATH/MISC/GridSearch.h>
42
43 #include <vector>
44 #include <functional>
45 #include <boost/optional.hpp>
46
47 namespace OpenMS
48 {
49 class ConsensusMap;
50 namespace Internal
51 {
52 class IDBoostGraph;
53 }
54 class PeptideIdentification;
55 class ProteinIdentification;
56
75 class OPENMS_DLLAPI BayesianProteinInferenceAlgorithm :
76 public DefaultParamHandler,
77 public ProgressLogger
78 {
79 public:
81 explicit BayesianProteinInferenceAlgorithm(unsigned int debug_lvl = 0);
82
84 ~BayesianProteinInferenceAlgorithm() override = default;
85
86 void updateMembers_() override;
87
90 class GraphInferenceFunctor;
91
95 class ExtendedGraphInferenceFunctor;
96
98 struct GridSearchEvaluator;
99
106 void inferPosteriorProbabilities(
107 std::vector<ProteinIdentification>& proteinIDs,
108 std::vector<PeptideIdentification>& peptideIDs,
109 boost::optional<const ExperimentalDesign> exp_des = boost::optional<const ExperimentalDesign>());
110
115 void inferPosteriorProbabilities(
116 ConsensusMap& cmap,
117 boost::optional<const ExperimentalDesign> exp_des = boost::optional<const ExperimentalDesign>());
118
119 private:
120
123 void inferPosteriorProbabilities_(Internal::IDBoostGraph& ibg);
124
126 GridSearch<double,double,double> initGridSearchFromParams_(
127 std::vector<double>& alpha_search,
128 std::vector<double>& beta_search,
129 std::vector<double>& gamma_search
130 );
131
133 void setScoreTypeAndSettings_(ProteinIdentification& proteinIDs);
134
137 std::function<void(PeptideIdentification&/*, const String& run_id*/)> checkConvertAndFilterPepHits_;
138
139 unsigned int debug_lvl_;
140
141 #ifdef INFERENCE_BENCH
142 std::vector<std::pair<double,Size>> debug_times_;
143 #endif
144
145 };
146 }
OpenMS::GridSearch
Definition: GridSearch.h:99
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
OpenMS::Internal::IDBoostGraph
Creates and maintains a boost graph based on the OpenMS ID datastructures.
Definition: IDBoostGraph.h:78
OpenMS::BayesianProteinInferenceAlgorithm
Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimenta...
Definition: BayesianProteinInferenceAlgorithm.h:75
GridSearch.h
ExperimentalDesign.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::BayesianProteinInferenceAlgorithm::checkConvertAndFilterPepHits_
std::function< void(PeptideIdentification &)> checkConvertAndFilterPepHits_
Definition: BayesianProteinInferenceAlgorithm.h:137
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
DefaultParamHandler.h
OpenMS::BayesianProteinInferenceAlgorithm::debug_lvl_
unsigned int debug_lvl_
Definition: BayesianProteinInferenceAlgorithm.h:139
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79