OpenMS  2.5.0
BayesianProteinInferenceAlgorithm.h
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31 // $Maintainer: Julianus Pfeuffer $
32 // $Authors: Julianus Pfeuffer $
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34 #pragma once
35 
36 //#define INFERENCE_BENCH
37 
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 }
DefaultParamHandler.h
OpenMS::BayesianProteinInferenceAlgorithm
Performs a Bayesian protein inference on Protein/Peptide identifications or ConsensusMap (experimenta...
Definition: BayesianProteinInferenceAlgorithm.h:75
OpenMS::BayesianProteinInferenceAlgorithm::checkConvertAndFilterPepHits_
std::function< void(PeptideIdentification &)> checkConvertAndFilterPepHits_
Definition: BayesianProteinInferenceAlgorithm.h:137
GridSearch.h
OpenMS::ProteinIdentification
Representation of a protein identification run.
Definition: ProteinIdentification.h:71
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
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
ProgressLogger.h
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
ExperimentalDesign.h
OpenMS::PeptideIdentification
Represents the peptide hits for a spectrum.
Definition: PeptideIdentification.h:62
OpenMS::GridSearch
Definition: GridSearch.h:99
OpenMS::BayesianProteinInferenceAlgorithm::debug_lvl_
unsigned int debug_lvl_
Definition: BayesianProteinInferenceAlgorithm.h:139
OpenMS::Internal::IDBoostGraph
Creates and maintains a boost graph based on the OpenMS ID datastructures.
Definition: IDBoostGraph.h:78