FLASHDeconvSpectrumFile.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2021.
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// $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 decoy);
 
    static void writeDeconvolvedMasses(DeconvolvedSpectrum& dspec, std::fstream& fs,
                                       const String& file_name,
                                       const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg,
                                       double tol,
                                       bool write_detail,
                                       bool decoy);
 
    //      @param avg averagine information to calculate monoisotopic and average mass difference
    static void writeTopFD(const DeconvolvedSpectrum& dspec, std::fstream& fs,
                           double snr_threshold = 1.0,
                           double decoy_harmonic_factor = 1.0,
                           double decoy_precursor_offset = .0);
 
  private:
 
    static const int topFD_min_peak_count_ = 3;
    static const int topFD_max_peak_count_ = 500;
 
  };
}// namespace OpenMS