OpenMS
FLASHDeconvSpectrumFile.h
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1 // Copyright (c) 2002-2023, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Kyowon Jeong $
6 // $Authors: Kyowon Jeong $
7 // --------------------------------------------------------------------------
8 #pragma once
9 
10 #include <OpenMS/config.h>
13 
14 #include <iomanip>
15 
16 namespace OpenMS
17 {
23  class OPENMS_DLLAPI FLASHDeconvSpectrumFile
24  {
25  public:
33  static void writeDeconvolvedMassesHeader(std::fstream& fs,
34  uint ms_level,
35  bool detail,
36  bool dummy);
37 
60  DeconvolvedSpectrum& target_spec,
61  std::fstream& fs,
62  const String& file_name,
64  double tol,
65  bool write_detail,
66  bool record_dummy);
67 
77  // @param avg averagine information to calculate monoisotopic and average mass difference
78  static void writeTopFD(DeconvolvedSpectrum& dspec, std::fstream& fs,
79  double snr_threshold = 1.0,
80  const uint min_ms_level = 1,
81  bool randomize_precursor_mass = false,
82  bool randomize_fragment_mass = false);
83 
84  private:
85 
87  static const int topFD_min_peak_count_ = 3;
89  static const int topFD_max_peak_count_ = 500;
90 
91  };
92 }// namespace OpenMS
A class representing a deconvolved spectrum. DeconvolvedSpectrum consists of PeakGroups representing ...
Definition: DeconvolvedSpectrum.h:30
Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine c...
Definition: FLASHDeconvHelperStructs.h:34
FLASHDeconv Spectrum level output *.tsv, *.msalign (for TopPIC) file formats.
Definition: FLASHDeconvSpectrumFile.h:24
static void writeTopFD(DeconvolvedSpectrum &dspec, std::fstream &fs, double snr_threshold=1.0, const uint min_ms_level=1, bool randomize_precursor_mass=false, bool randomize_fragment_mass=false)
write the deconvolved masses TopFD output (*.msalign)
static void writeDeconvolvedMassesHeader(std::fstream &fs, uint ms_level, bool detail, bool dummy)
write the header in the tsv output file (spectrum level)
static void writeDeconvolvedMasses(DeconvolvedSpectrum &dspec, DeconvolvedSpectrum &target_spec, std::fstream &fs, const String &file_name, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, double tol, bool write_detail, bool record_dummy)
write the deconvolved masses in the output file (spectrum level)
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22