OpenMS  2.5.0
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 
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::MapAlignmentTransformer
This class collects functions for applying retention time transformations to data structures.
Definition: MapAlignmentTransformer.h:56
OpenMS::BaseFeature
A basic LC-MS feature.
Definition: BaseFeature.h:56
OpenMS::MSExperiment
In-Memory representation of a mass spectrometry experiment.
Definition: MSExperiment.h:77
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
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:79
MSExperiment.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::Feature
An LC-MS feature.
Definition: Feature.h:70
MetaInfoInterface.h
OpenMS::TransformationDescription
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:61
StandardTypes.h