| OpenMS 2.5.0

MapAlignmentTransformer.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: Timo Sachsenberg $
32 // $Authors: Stephan Aiche $
33 // --------------------------------------------------------------------------
34
35
36 #pragma once
37
38 #include <vector>
39 #include <OpenMS/config.h>
40
41 #include <OpenMS/KERNEL/StandardTypes.h>
42 #include <OpenMS/KERNEL/MSExperiment.h>
43 #include <OpenMS/KERNEL/FeatureMap.h>
44 #include <OpenMS/METADATA/MetaInfoInterface.h>
45
46 namespace OpenMS
47 {
48 class TransformationDescription;
49 class ConsensusMap;
50 class PeptideIdentification;
51 class ConsensusFeature;
52
56 class OPENMS_DLLAPI MapAlignmentTransformer
57 {
58
59 public:
61 static void transformRetentionTimes(PeakMap& msexp,
62 const TransformationDescription& trafo,
63 bool store_original_rt = false);
64
66 static void transformRetentionTimes(
67 FeatureMap& fmap, const TransformationDescription& trafo,
68 bool store_original_rt = false);
69
71 static void transformRetentionTimes(
72 ConsensusMap& cmap, const TransformationDescription& trafo,
73 bool store_original_rt = false);
74
76 static void transformRetentionTimes(
77 std::vector<PeptideIdentification>& pep_ids,
78 const TransformationDescription& trafo, bool store_original_rt = false);
79
80 private:
82 static void applyToFeature_(Feature& feature,
83 const TransformationDescription& trafo,
84 bool store_original_rt = false);
85
87 static void applyToBaseFeature_(BaseFeature& feature,
88 const TransformationDescription& trafo,
89 bool store_original_rt = false);
90
92 static void applyToConsensusFeature_(
93 ConsensusFeature& feature, const TransformationDescription& trafo,
94 bool store_original_rt = false);
95
103 static bool storeOriginalRT_(MetaInfoInterface& meta_info,
104 double original_rt);
105
106 };
107 } // namespace OpenMS
108
109
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
StandardTypes.h
OpenMS::ConsensusFeature
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:69
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
FeatureMap.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
MSExperiment.h
OpenMS::ConsensusMap
A container for consensus elements.
Definition: ConsensusMap.h:79
MetaInfoInterface.h
OpenMS::MapAlignmentTransformer
This class collects functions for applying retention time transformations to data structures...
Definition: MapAlignmentTransformer.h:56
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:56