FLASHDeconvSpectrumFile.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: Kyowon Jeong $
// $Authors: Kyowon Jeong $
// --------------------------------------------------------------------------
#pragma once
 
#include <OpenMS/ANALYSIS/TOPDOWN/DeconvolvedSpectrum.h>
#include <OpenMS/ANALYSIS/TOPDOWN/FLASHHelperClasses.h>
#include <OpenMS/config.h>
#include <iomanip>
 
namespace OpenMS
{
  class OPENMS_DLLAPI FLASHDeconvSpectrumFile
  {
  public:
    static void writeDeconvolvedMassesHeader(std::ostream& os,
                                             uint ms_level,
                                             bool detail,
                                             bool report_decoy);
    static void writeDeconvolvedMasses(const DeconvolvedSpectrum& dspec,
                                       std::ostream& os,
                                       const String& file_name,
                                       const FLASHHelperClasses::PrecalculatedAveragine& avg,
                                       const FLASHHelperClasses::PrecalculatedAveragine& decoy_avg,
                                       double tol,
                                       bool write_detail,
                                       bool record_decoy, double noise_decoy_weight);
 
    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::ostream& os, std::vector<DeconvolvedSpectrum>& deconvolved_spectra);
 
    static void writeTopFDHeader(std::ostream& os, const Param& param);
 
    static void writeTopFD(const DeconvolvedSpectrum& dspec, std::ostream& os, const String& filename,
                           double qval_threshold = 1.0,
                           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