RNAPrecursorCorrector.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: Sam Wein $
// $Authors: Sam Wein $
// --------------------------------------------------------------------------
#pragma once
 
#include "RNADirectedDeconvolution.h"
#include <OpenMS/KERNEL/MSExperiment.h>
 
namespace OpenMS
{
  class RNAPrecursorCorrector
  {
  public:
    struct Result
    {
      std::string spectrum, parent, parent_source, status = "no_envelope";
      double original_mz = 0, corrected_mz = 0, mono_mass = 0, cosine = 0, snr = 0;
      double selected_error_ppm = 0;
      int original_charge = 0, charge = 0, isotope = -1;
      Size parent_peak_count = 0, parent_query_count = 0;
      bool mono_observed = false;
 
      bool accepted() const { return status == "corrected" || status == "monoisotopic"; }
    };
 
    RNAPrecursorCorrector(double tolerance_ppm, int min_abs_charge, int max_abs_charge,
                          bool positive, double max_mass = 1000.0,
                          double min_cos = 0.85, double min_snr = 0.25);
 
    Result match(const DeconvolvedSpectrum& groups, const Precursor& precursor) const;
 
    std::vector<Result> correct(MSExperiment& experiment);
 
    static void storeReport(const std::string& filename, const std::vector<Result>& results);
 
  private:
    RNADirectedDeconvolution detector_;
    double tolerance_ppm_, min_cos_, min_snr_;
    int min_abs_charge_, max_abs_charge_;
    bool positive_;
  };
}