OpenMS
FLASHDeconvFeatureFile.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 
9 
10 #pragma once
11 
14 #include <OpenMS/config.h>
15 #include <iomanip>
16 #include <iostream>
17 
18 
19 namespace OpenMS
20 {
26  class OPENMS_DLLAPI FLASHDeconvFeatureFile
27  {
28  public:
30  static void writeHeader(std::fstream& fs);
31 
33  static void writePromexHeader(std::fstream& fs);
34 
36  static void writeTopFDFeatureHeader(std::vector<std::fstream>& fs);
37 
39  static void writeFeatures(const std::vector<FLASHDeconvHelperStructs::MassFeature>& mass_features, const String& file_name, std::fstream& fs);
40 
41 
51  static void writeTopFDFeatures(const std::vector<FLASHDeconvHelperStructs::MassFeature>& mass_features, const std::map<int, PeakGroup>& precursor_peak_groups,
52  const std::map<int, double>& scan_rt_map, const String& file_name, std::vector<std::fstream>& fs);
53 
63  static void writePromexFeatures(const std::vector<FLASHDeconvHelperStructs::MassFeature>& mass_features, const std::map<int, PeakGroup>& precursor_peak_groups,
64  const std::map<int, double>& scan_rt_map, const FLASHDeconvHelperStructs::PrecalculatedAveragine& avg, std::fstream& fs);
65  };
66 } // namespace OpenMS
FLASHDeconv feature level output *.tsv, *.ms1ft (for Promex), *.feature (for TopPIC) file formats.
Definition: FLASHDeconvFeatureFile.h:27
static void writeHeader(std::fstream &fs)
write header line for regular file output
static void writeFeatures(const std::vector< FLASHDeconvHelperStructs::MassFeature > &mass_features, const String &file_name, std::fstream &fs)
write the features in regular file output
static void writePromexHeader(std::fstream &fs)
write header line for promex file output
static void writeTopFDFeatures(const std::vector< FLASHDeconvHelperStructs::MassFeature > &mass_features, const std::map< int, PeakGroup > &precursor_peak_groups, const std::map< int, double > &scan_rt_map, const String &file_name, std::vector< std::fstream > &fs)
Find mass features and write features in TopFD format files.
static void writePromexFeatures(const std::vector< FLASHDeconvHelperStructs::MassFeature > &mass_features, const std::map< int, PeakGroup > &precursor_peak_groups, const std::map< int, double > &scan_rt_map, const FLASHDeconvHelperStructs::PrecalculatedAveragine &avg, std::fstream &fs)
Find mass features and write features in Promex format files.
static void writeTopFDFeatureHeader(std::vector< std::fstream > &fs)
write header line for topFD feature files
Averagine patterns pre-calculated for speed up. Other variables are also calculated for fast cosine c...
Definition: FLASHDeconvHelperStructs.h:34
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:22