OpenSwathPeptidoformInference.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Justin Sing $
// $Authors: Justin Sing $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathInferenceConfig.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathInferenceData.h>
#include <OpenMS/config.h>
 
#include <vector>
 
namespace OpenMS
{
  class OpenSwathPeptidoformInference
  {
  public:
    struct BayesianModelRow
    {
      Int64 feature_id = -1;
      Int64 hypothesis = -1;
      double prior = 0.0;
      double evidence = 0.0;
    };
 
    struct PosteriorRow
    {
      Int64 feature_id = -1;
      Int64 hypothesis = -1;
      double posterior = 0.0;
    };
 
    static std::vector<double> computeModelFDR(const std::vector<double>& pep_values);
 
    static std::vector<BayesianModelRow> preparePrecursorBM(const std::vector<IPFPrecursorRow>& rows);
 
    static std::vector<PosteriorRow> applyBM(const std::vector<BayesianModelRow>& rows);
 
    std::vector<IPFPrecursorProbabilityRow> precursorInference(const std::vector<IPFPrecursorRow>& precursor_rows,
                                                               const PeptidoformInferenceConfig& config) const;
 
    std::vector<IPFResultRow> infer(const std::vector<IPFPrecursorRow>& precursor_rows,
                                    const std::vector<IPFTransitionRow>& transition_rows,
                                    const std::vector<IPFAlignmentRow>& alignment_rows,
                                    const PeptidoformInferenceConfig& config) const;
  };
} // namespace OpenMS