OpenMS
MapAlignmentTransformer.h
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1 // Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
2 // SPDX-License-Identifier: BSD-3-Clause
3 //
4 // --------------------------------------------------------------------------
5 // $Maintainer: Timo Sachsenberg $
6 // $Authors: Stephan Aiche $
7 // --------------------------------------------------------------------------
8 
9 
10 #pragma once
11 
12 #include <vector>
13 #include <OpenMS/config.h>
14 
20 
21 namespace OpenMS
22 {
23  class TransformationDescription;
24  class ConsensusMap;
25  class PeptideIdentification;
26  class ConsensusFeature;
27 
31  class OPENMS_DLLAPI MapAlignmentTransformer
32  {
33 
34  public:
36  static void transformRetentionTimes(PeakMap& msexp,
37  const TransformationDescription& trafo,
38  bool store_original_rt = false);
39 
42  const TransformationDescription& trafo,
43  bool store_original_rt = false);
44 
47  const TransformationDescription& trafo,
48  bool store_original_rt = false);
49 
52  std::vector<PeptideIdentification>& pep_ids,
53  const TransformationDescription& trafo, bool store_original_rt = false);
54 
57  const TransformationDescription& trafo,
58  bool store_original_rt = false);
59 
60  private:
62  static void applyToFeature_(Feature& feature,
63  const TransformationDescription& trafo,
64  bool store_original_rt = false);
65 
67  static void applyToBaseFeature_(BaseFeature& feature,
68  const TransformationDescription& trafo,
69  bool store_original_rt = false);
70 
73  ConsensusFeature& feature, const TransformationDescription& trafo,
74  bool store_original_rt = false);
75 
83  static bool storeOriginalRT_(MetaInfoInterface& meta_info,
84  double original_rt);
85 
86  };
87 } // namespace OpenMS
88 
89 
A basic LC-MS feature.
Definition: BaseFeature.h:33
A consensus feature spanning multiple LC-MS/MS experiments.
Definition: ConsensusFeature.h:45
A container for consensus elements.
Definition: ConsensusMap.h:66
A container for features.
Definition: FeatureMap.h:80
An LC-MS feature.
Definition: Feature.h:46
Definition: IdentificationData.h:87
In-Memory representation of a mass spectrometry run.
Definition: MSExperiment.h:45
This class collects functions for applying retention time transformations to data structures.
Definition: MapAlignmentTransformer.h:32
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:35
Generic description of a coordinate transformation.
Definition: TransformationDescription.h:37
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19