BayesianProteinInferenceAlgorithm.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
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//    may be used to endorse or promote products derived from this software
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// --------------------------------------------------------------------------
// $Maintainer: Julianus Pfeuffer $
// $Authors: Julianus Pfeuffer $
// --------------------------------------------------------------------------
#pragma once

//#define INFERENCE_BENCH

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/METADATA/ExperimentalDesign.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/MATH/MISC/GridSearch.h>

#include <vector>
#include <functional>
#include <optional>

namespace OpenMS
{
  class ConsensusMap;
  namespace Internal
  {
    class IDBoostGraph;
  }
  class PeptideIdentification;
  class ProteinIdentification;

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

    ~BayesianProteinInferenceAlgorithm() override = default;

    void updateMembers_() override;

    class GraphInferenceFunctor;

    class ExtendedGraphInferenceFunctor;

    struct GridSearchEvaluator;


    void inferPosteriorProbabilities(
        std::vector<ProteinIdentification>& proteinIDs,
        std::vector<PeptideIdentification>& peptideIDs,
        bool greedy_group_resolution,
        std::optional<const ExperimentalDesign> exp_des = std::optional<const ExperimentalDesign>());

    void inferPosteriorProbabilities(
        ConsensusMap& cmap,
        bool greedy_group_resolution,
        std::optional<const ExperimentalDesign> exp_des = std::optional<const ExperimentalDesign>());

  private:

    void inferPosteriorProbabilities_(Internal::IDBoostGraph& ibg);

    GridSearch<double,double,double> initGridSearchFromParams_(
        std::vector<double>& alpha_search,
        std::vector<double>& beta_search,
        std::vector<double>& gamma_search
        );

    void setScoreTypeAndSettings_(ProteinIdentification& proteinIDs);

    // TODO double-check if -1 is maybe the better option
    //  to distinguish between "untouched/unused/unreferenced" (e.g. if somehow
    //  not removed/filtered) and an inferred probability of 0.0. But it might give
    //  problems in FDR algorithms if not ignored/removed correctly
    void resetProteinScores_(ProteinIdentification& protein_id, bool keep_old_as_prior);

    std::function<void(PeptideIdentification&/*, const String& run_id*/)> checkConvertAndFilterPepHits_;

    unsigned int debug_lvl_;

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

  };
}