TransitionListEvidenceFilter.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/OpenSwathWorkflow.h>
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/SwathMap.h>
#include <OpenMS/OPENSWATHALGO/DATAACCESS/TransitionExperiment.h>
 
#include <string>
#include <vector>
 
namespace OpenMS
{
  class OPENMS_DLLAPI TransitionListEvidenceFilter :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    struct PrecursorEvidence
    {
      std::string compound_id;
      std::string sequence;
      double precursor_mz{0.0};
      double precursor_im{-1.0};
      bool supported_ms1{false};
      bool supported_ms2{false};
      Size ms1_hit_count{0};
      double ms1_max_intensity{0.0};
      double ms1_sum_intensity{0.0};
      double ms1_best_rt{-1.0};
      Size ms2_hit_count{0};
      Size ms2_best_fragment_hits{0};
      double ms2_max_intensity{0.0};
      double ms2_sum_intensity{0.0};
      double ms2_best_rt{-1.0};
    };
 
    struct Result
    {
      OpenSwath::LightTargetedExperiment filtered_targets;
      std::vector<PrecursorEvidence> evidence;
      Size total_target_precursors{0};
      Size supported_precursors{0};
      Size ms1_supported{0};
      Size ms2_supported{0};
      Size hybrid_supported{0};
      std::string summary;
      double precursor_im_scale{1.0};
      bool precursor_im_scaled_by_charge{false};
    };
 
    TransitionListEvidenceFilter();
 
    ~TransitionListEvidenceFilter() override = default;
 
    void updateMembers_() override;
 
    Result filter(const std::vector<OpenSwath::SwathMap>& swath_maps,
                  const OpenSwath::LightTargetedExperiment& transition_exp,
                  const ChromExtractParams& ms1_params,
                  const ChromExtractParams& ms2_params,
                  bool pasef,
                  int threads = 1) const;
 
private:
    bool enabled_{false};
    std::string evidence_sources_{"hybrid"};
    Size ms1_top_peaks_per_spectrum_{1000};
    Size ms2_top_peaks_per_spectrum_{1000};
    Size ms2_top_transitions_per_precursor_{6};
    Size ms2_min_fragment_hits_{4};
    Size min_supported_precursors_{3};
    bool peak_picking_enabled_{false};
    bool peak_picking_use_gauss_{true};
  };
}