FLASHDeconvSpectrumFile.h

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// Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Kyowon Jeong $
// $Authors: Kyowon Jeong $
// --------------------------------------------------------------------------
#pragma once
 
#include <OpenMS/config.h>
#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHDeconvHelperStructs.h>
 
#include <iomanip>
 
namespace OpenMS
{
  class OPENMS_DLLAPI FLASHDeconvSpectrumFile
  {
  public:
    static void writeDeconvolvedMassesHeader(std::fstream& fs,
                                             uint ms_level,
                                             bool detail,
                                             bool report_decoy);
 
    static void writeDeconvolvedMasses(DeconvolvedSpectrum& dspec,
                                       std::fstream& fs,
                                       const String& file_name,
                                       const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg,
                                       double tol,
                                       bool write_detail,
                                       bool record_decoy);
 
    static void writeMzML(const MSExperiment& map, std::vector<DeconvolvedSpectrum>& deconvolved_spectra, const String& deconvolved_mzML_file, const String& annotated_mzML_file, int mzml_charge, DoubleList tols);
 
    static void writeIsobaricQuantification(std::fstream& fs, std::vector<DeconvolvedSpectrum>& deconvolved_spectra);
 
    static void writeDLMatrixHeader(std::fstream& fs);
 
    static void writeDLMatrix(std::vector<DeconvolvedSpectrum>& dspecs, double tol, std::fstream& fs, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg);
 
    static void writeTopFDHeader(std::fstream& fs, const Param& param);
 
    //      @param avg averagine information to calculate monoisotopic and average mass difference
    static void writeTopFD(DeconvolvedSpectrum& dspec, std::fstream& fs, const String& filename,
                           const double snr_threshold = 1.0,
                           const double qval_threshold = 1.0,
                           const uint min_ms_level = 1,
                           bool randomize_precursor_mass = false,
                           bool randomize_fragment_mass = false);
 
  private:
 
    static const int topFD_min_peak_count_ = 3;
    static const int topFD_max_peak_count_ = 500;
 
  };
}// namespace OpenMS