OpenMS  3.0.0
MQEvidenceExporter.h
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31 // $Maintainer: Chris Bielow$
32 // $Authors: Valentin Noske, Vincent Musch$
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34 
35 #pragma once
36 
37 #include <fstream>
40 #include <OpenMS/KERNEL/Feature.h>
42 
43 class OPENMS_DLLAPI MQEvidence
57 {
58 private:
59  std::fstream file_;
60  OpenMS::Size id_ = 0;
61  std::map<OpenMS::String, OpenMS::Size> protein_id_;
63 
67  void exportHeader_();
68 
81  OpenMS::Size proteinGroupID_(const OpenMS::String& protein_accession);
82 
93  std::map<OpenMS::Size, OpenMS::Size> makeFeatureUIDtoConsensusMapIndex_(const OpenMS::ConsensusMap& cmap);
94 
108  bool hasValidPepID_(
109  const OpenMS::Feature& f,
110  const OpenMS::Size c_feature_number,
111  const std::multimap<OpenMS::String, std::pair<OpenMS::Size, OpenMS::Size>>& UIDs,
113 
124  bool hasPeptideIdentifications_(const OpenMS::ConsensusFeature& cf);
125 
140  void exportRowFromFeature_(
141  const OpenMS::Feature& f,
142  const OpenMS::ConsensusMap& cmap,
143  const OpenMS::Size c_feature_number,
144  const OpenMS::String& raw_file,
145  const std::multimap<OpenMS::String, std::pair<OpenMS::Size, OpenMS::Size>>& UIDs,
147 
148 public:
161  explicit MQEvidence(const OpenMS::String& path);
162 
166  ~MQEvidence();
167 
174  bool isValid();
175 
187  void exportFeatureMap(
188  const OpenMS::FeatureMap& feature_map,
189  const OpenMS::ConsensusMap& cmap);
190 };
MQEvidence::protein_id_
std::map< OpenMS::String, OpenMS::Size > protein_id_
map that maps each accession to its distinct number in this evidence.txt
Definition: MQEvidenceExporter.h:61
OpenMS::String
A more convenient string class.
Definition: String.h:58
MQEvidence::file_
std::fstream file_
Stream where the data is added to create evidence.txt.
Definition: MQEvidenceExporter.h:59
Feature.h
ConsensusMap.h
OpenMS::Size
size_t Size
Size type e.g. used as variable which can hold result of size()
Definition: Types.h:127
OpenMS::ProteinIdentification::Mapping
two way mapping from ms-run-path to protID|pepID-identifier
Definition: ProteinIdentification.h:78
ConsensusFeature.h
MQEvidence::filename_
OpenMS::String filename_
path and name of the evidence.txt
Definition: MQEvidenceExporter.h:62
FeatureMap.h
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:82
MQEvidence
Builds a MaxQuant Evidence.txt.
Definition: MQEvidenceExporter.h:43
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70