BayesianProteinInferenceAlgorithm.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
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#ifndef OPENMS_ANALYSIS_ID_BAYESIANPROTEININFERENCE_H
#define OPENMS_ANALYSIS_ID_BAYESIANPROTEININFERENCE_H

//#define INFERENCE_BENCH

#include <OpenMS/ANALYSIS/ID/MessagePasserFactory.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/MATH/MISC/GridSearch.h>
#include <vector>

namespace OpenMS
{
  class OPENMS_DLLAPI BayesianProteinInferenceAlgorithm :
      public DefaultParamHandler,
      public ProgressLogger
  {
  public:
    explicit BayesianProteinInferenceAlgorithm(unsigned int debug_lvl = 0);

    ~BayesianProteinInferenceAlgorithm() override = default;

    class GraphInferenceFunctor;

    class ExtendedGraphInferenceFunctor;


    class GraphInferenceFunctorNoGroups;

    struct GridSearchEvaluator;

    void inferPosteriorProbabilities(std::vector<ProteinIdentification>& proteinIDs, std::vector<PeptideIdentification>& peptideIDs);

    void inferPosteriorProbabilities(const StringList& idXMLs, const String db,const ExperimentalDesign& expDesign, ProteinIdentification& proteinIDs, std::vector<PeptideIdentification>& peptideIDs);
    void inferPosteriorProbabilities(std::vector<PeptideIdentification> pepIdReplicates, ProteinIdentification& proteinIds, const String& db);

  private:
    class AnnotateIndistGroupsFunctor;

    GridSearch<double,double,double> grid{{0.008,0.032,0.128},{0.001},{0.5}};

    unsigned int debug_lvl_;

    #ifdef INFERENCE_BENCH
    std::vector<std::pair<double,Size>> debug_times_;
    #endif

  };
}
#endif // OPENMS_ANALYSIS_ID_BAYESIANPROTEININFERENCE_H