OpenMS
GNPSMGFFile.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Dorrestein Lab - University of California San Diego - https://dorresteinlab.ucsd.edu/$
6 // $Authors: Abinesh Sarvepalli and Louis Felix Nothias$
7 // $Contributors: Fabian Aicheler and Oliver Alka from Oliver Kohlbacher's group at Tubingen University$
8 
9 #pragma once
10 
14 
15 namespace OpenMS
16 {
17  class OPENMS_DLLAPI GNPSMGFFile :
18  public DefaultParamHandler,
19  public ProgressLogger
20  {
21  public:
22  // default c'tor
24 
25  // see GNPSExport tool documentation
32  void store(const String& consensus_file_path, const StringList& mzml_file_paths, const String& out) const;
33 
34  private:
35  static constexpr double DEF_COSINE_SIMILARITY = 0.9;
36  static constexpr double DEF_MERGE_BIN_SIZE = static_cast<double>(BinnedSpectrum::DEFAULT_BIN_WIDTH_HIRES);
37 
38 // static constexpr double DEF_PREC_MASS_TOL = 0.5;
39 // static constexpr bool DEF_PREC_MASS_TOL_ISPPM = false;
40 
41  static constexpr int DEF_PEPT_CUTOFF = 5;
42  static constexpr int DEF_MSMAP_CACHE = 50;
43  };
44 }
static constexpr const float DEFAULT_BIN_WIDTH_HIRES
Definition: BinnedSpectrum.h:78
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
Definition: GNPSMGFFile.h:20
void store(const String &consensus_file_path, const StringList &mzml_file_paths, const String &out) const
Create file for GNPS molecular networking.
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
A more convenient string class.
Definition: String.h:34
std::vector< String > StringList
Vector of String.
Definition: ListUtils.h:44
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19