| OpenMS 2.5.0

MRMFeature.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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4 // Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
5 // ETH Zurich, and Freie Universitaet Berlin 2002-2020.
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Hannes Roest $
32 // $Authors: Hannes Roest $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/KERNEL/Feature.h>
38 #include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>
39
40 namespace OpenMS
41 {
50 class OPENMS_DLLAPI MRMFeature :
51 public Feature
52 {
53 public:
54
56
57 typedef std::vector<Feature> FeatureListType;
60
62
63 MRMFeature();
65
67 MRMFeature(const MRMFeature &rhs);
68
70 MRMFeature(MRMFeature &&rhs) = default;
71
73 MRMFeature & operator=(const MRMFeature & rhs);
74
76 MRMFeature& operator=(MRMFeature&&) & = default;
77
79 ~MRMFeature() override;
81
83
84
86 const OpenSwath_Scores & getScores() const;
87
89 OpenSwath_Scores & getScores();
90
92 Feature & getFeature(const String& key);
93
95 const Feature & getFeature(const String& key) const;
96
98 void setScores(const OpenSwath_Scores & scores);
99
101 void addScore(const String & score_name, double score);
102
104 void addFeature(const Feature & feature, const String& key);
105
106 void addFeature(Feature && feature, const String& key);
107
109 const std::vector<Feature> & getFeatures() const;
110
112 void getFeatureIDs(std::vector<String> & result) const;
113
115 void addPrecursorFeature(const Feature & feature, const String& key);
116
117 void addPrecursorFeature(Feature && feature, const String& key);
118
120 void getPrecursorFeatureIDs(std::vector<String> & result) const;
121
123 Feature & getPrecursorFeature(String key);
124
126 const Feature & getPrecursorFeature(String key) const;
127
128 void IDScoresAsMetaValue(bool decoy, const OpenSwath_Ind_Scores& idscores);
130
131 protected:
132
133 FeatureListType features_;
134
135 FeatureListType precursor_features_;
136
138 OpenSwath_Scores pg_scores_;
139
141 std::map<String, int> feature_map_;
142
144 std::map<String, int> precursor_feature_map_;
145
146 };
147 }
148
149
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::MRMFeature::precursor_features_
FeatureListType precursor_features_
Definition: MRMFeature.h:135
OpenMS::String
A more convenient string class.
Definition: String.h:58
Feature.h
OpenSwathScores.h
OpenMS::MRMFeature::FeatureListType
std::vector< Feature > FeatureListType
Type definitions.
Definition: MRMFeature.h:58
OpenMS::OpenSwath_Ind_Scores
Definition: OpenSwathScores.h:192
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::OpenSwath_Scores
A structure to hold the different scores computed by OpenSWATH.
Definition: OpenSwathScores.h:80
OpenMS::MRMFeature::precursor_feature_map_
std::map< String, int > precursor_feature_map_
map native ids to the precursor features
Definition: MRMFeature.h:144
OpenMS::MRMFeature::pg_scores_
OpenSwath_Scores pg_scores_
peak group scores
Definition: MRMFeature.h:138
OpenMS::MRMFeature
A multi-chromatogram MRM feature.
Definition: MRMFeature.h:50
OpenMS::MRMFeature::feature_map_
std::map< String, int > feature_map_
map native ids to the features
Definition: MRMFeature.h:141
OpenMS::MRMFeature::features_
FeatureListType features_
Definition: MRMFeature.h:133