OpenMS
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 
68  const TransformationDescription& trafo,
69  bool store_original_rt = false);
70 
73  const TransformationDescription& trafo,
74  bool store_original_rt = false);
75 
78  std::vector<PeptideIdentification>& pep_ids,
79  const TransformationDescription& trafo, bool store_original_rt = false);
80 
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 
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 
A basic LC-MS feature.
Definition: BaseFeature.h:59
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:71
A container for consensus elements.
Definition: ConsensusMap.h:92
A container for features.
Definition: FeatureMap.h:106
An LC-MS feature.
Definition: Feature.h:72
Definition: IdentificationData.h:113
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:72
This class collects functions for applying retention time transformations to data structures.
Definition: MapAlignmentTransformer.h:58
static void transformRetentionTimes(IdentificationData &id_data, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to input items in IdentificationData.
static void transformRetentionTimes(ConsensusMap &cmap, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to a consensus map.
static void applyToBaseFeature_(BaseFeature &feature, const TransformationDescription &trafo, bool store_original_rt=false)
Applies a transformation to a basic feature.
static void transformRetentionTimes(PeakMap &msexp, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to a peak map.
static void applyToConsensusFeature_(ConsensusFeature &feature, const TransformationDescription &trafo, bool store_original_rt=false)
Applies a transformation to a consensus feature.
static bool storeOriginalRT_(MetaInfoInterface &meta_info, double original_rt)
Stores the original RT in a meta value.
static void transformRetentionTimes(FeatureMap &fmap, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to a feature map.
static void transformRetentionTimes(std::vector< PeptideIdentification > &pep_ids, const TransformationDescription &trafo, bool store_original_rt=false)
Applies the given transformation to peptide identifications.
static void applyToFeature_(Feature &feature, const TransformationDescription &trafo, bool store_original_rt=false)
Applies a transformation to a feature.
Interface for classes that can store arbitrary meta information (Type-Name-Value tuples).
Definition: MetaInfoInterface.h:61
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:63
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:48