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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 // $Maintainer: Chris Bielow$
6 // $Authors: Valentin Noske, Vincent Musch$
7 // --------------------------------------------------------------------------
9 #pragma once
11 #include <fstream>
14 #include <OpenMS/KERNEL/Feature.h>
19 #include <map>
21 class OPENMS_DLLAPI MQEvidence
35 {
36 private:
37  std::fstream file_;
38  OpenMS::Size id_ = 0;
44  void exportHeader_();
63  const OpenMS::Feature& f,
64  const OpenMS::ConsensusMap& cmap,
65  const OpenMS::Size c_feature_number,
66  const OpenMS::String& raw_file,
67  const std::multimap<OpenMS::String, std::pair<OpenMS::Size, OpenMS::Size>>& UIDs,
69  const OpenMS::MSExperiment& exp= {},
70  const std::map<OpenMS::String,OpenMS::String>& prot_map = {});
72 public:
85  explicit MQEvidence(const OpenMS::String& path);
106  const OpenMS::FeatureMap& feature_map,
107  const OpenMS::ConsensusMap& cmap,
108  const OpenMS::MSExperiment& exp= {},
109  const std::map<OpenMS::String,OpenMS::String>& prot_map = {});
110 };
Builds a MaxQuant Evidence.txt.
Definition: MQEvidenceExporter.h:35
MQEvidence(const OpenMS::String &path)
Creates MQEvidence object and evidence.txt in given path.
void exportFeatureMap(const OpenMS::FeatureMap &feature_map, const OpenMS::ConsensusMap &cmap, const OpenMS::MSExperiment &exp={}, const std::map< OpenMS::String, OpenMS::String > &prot_map={})
Exports a FeatureMap to the evidence.txt.
OpenMS::String filename_
path and name of the evidence.txt
Definition: MQEvidenceExporter.h:39
void exportRowFromFeature_(const OpenMS::Feature &f, const OpenMS::ConsensusMap &cmap, const OpenMS::Size c_feature_number, const OpenMS::String &raw_file, const std::multimap< OpenMS::String, std::pair< OpenMS::Size, OpenMS::Size >> &UIDs, const OpenMS::ProteinIdentification::Mapping &mp_f, const OpenMS::MSExperiment &exp={}, const std::map< OpenMS::String, OpenMS::String > &prot_map={})
Export one Feature as a row in MQEvidence.txt.
void exportHeader_()
Writes the header of evidence.txt (Names of columns)
Closes f_stream.
std::fstream file_
Stream where the data is added to create evidence.txt.
Definition: MQEvidenceExporter.h:37
A container for consensus elements.
Definition: ConsensusMap.h:66
A container for features.
Definition: FeatureMap.h:80
An LC-MS feature.
Definition: Feature.h:46
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:46
A more convenient string class.
Definition: String.h:34
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:101
two way mapping from ms-run-path to protID|pepID-identifier
Definition: ProteinIdentification.h:57