OpenMS  3.0.0
MapAlignmentTransformer.h
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31 // $Maintainer: Timo Sachsenberg $
32 // $Authors: Stephan Aiche $
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34 
35 
36 #pragma once
37 
38 #include <vector>
39 #include <OpenMS/config.h>
40 
46 
47 namespace OpenMS
48 {
49  class TransformationDescription;
50  class ConsensusMap;
51  class PeptideIdentification;
52  class ConsensusFeature;
53 
57  class OPENMS_DLLAPI MapAlignmentTransformer
58  {
59 
60  public:
62  static void transformRetentionTimes(PeakMap& msexp,
63  const TransformationDescription& trafo,
64  bool store_original_rt = false);
65 
67  static void transformRetentionTimes(FeatureMap& fmap,
68  const TransformationDescription& trafo,
69  bool store_original_rt = false);
70 
72  static void transformRetentionTimes(ConsensusMap& cmap,
73  const TransformationDescription& trafo,
74  bool store_original_rt = false);
75 
77  static void transformRetentionTimes(
78  std::vector<PeptideIdentification>& pep_ids,
79  const TransformationDescription& trafo, bool store_original_rt = false);
80 
82  static void transformRetentionTimes(IdentificationData& id_data,
83  const TransformationDescription& trafo,
84  bool store_original_rt = false);
85 
86  private:
88  static void applyToFeature_(Feature& feature,
89  const TransformationDescription& trafo,
90  bool store_original_rt = false);
91 
93  static void applyToBaseFeature_(BaseFeature& feature,
94  const TransformationDescription& trafo,
95  bool store_original_rt = false);
96 
98  static void applyToConsensusFeature_(
99  ConsensusFeature& feature, const TransformationDescription& trafo,
100  bool store_original_rt = false);
101 
109  static bool storeOriginalRT_(MetaInfoInterface& meta_info,
110  double original_rt);
111 
112  };
113 } // namespace OpenMS
114 
115 
OpenMS::MapAlignmentTransformer
This class collects functions for applying retention time transformations to data structures.
Definition: MapAlignmentTransformer.h:57
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:58
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:70
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::MetaInfoInterface
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:60
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
MSExperiment.h
OpenMS::IdentificationData
Representation of spectrum identification results and associated data.
Definition: IdentificationData.h:94
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
MetaInfoInterface.h
IdentificationData.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:62
StandardTypes.h