OpenMS
MapAlignmentAlgorithmTreeGuided.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 // $Maintainer: Julia Thueringer$
6 // $Authors: Julia Thueringer $
7 // --------------------------------------------------------------------------
8 
9 #pragma once
10 
15 
16 namespace OpenMS
17 {
44  class OPENMS_DLLAPI MapAlignmentAlgorithmTreeGuided :
45  public DefaultParamHandler,
46  public ProgressLogger
47  {
48 public:
51 
54 
62  static void buildTree(std::vector<FeatureMap>& feature_maps, std::vector<BinaryTreeNode>& tree, std::vector<std::vector<double>>& maps_ranges);
63 
73  void treeGuidedAlignment(const std::vector<BinaryTreeNode>& tree, std::vector<FeatureMap>& feature_maps_transformed,
74  std::vector<std::vector<double>>& maps_ranges, FeatureMap& map_transformed,
75  std::vector<Size>& trafo_order);
76 
80  void align(std::vector<FeatureMap>& data,
81  std::vector<TransformationDescription>& transformations);
82 
91  void computeTrafosByOriginalRT(std::vector<FeatureMap>& feature_maps, FeatureMap& map_transformed,
92  std::vector<TransformationDescription>& transformations, const std::vector<Size>& trafo_order);
93 
100  static void computeTransformedFeatureMaps(std::vector<FeatureMap>& feature_maps, const std::vector<TransformationDescription>& transformations);
101 
102 protected:
104  typedef std::map<String, DoubleList> SeqAndRTList;
105 
106  // Update defaults model_type_, model_param_ and align_algorithm_
107  void updateMembers_() override;
108 
111 
114 
117 
125  class PeptideIdentificationsPearsonDistance_;
126 
135  static void addPeptideSequences_(const std::vector<PeptideIdentification>& peptides, SeqAndRTList& peptide_rts,
136  std::vector<double>& map_range, double feature_rt);
137 
145  static void extractSeqAndRt_(const std::vector<FeatureMap>& feature_maps, std::vector<SeqAndRTList>& maps_seq_and_rt,
146  std::vector<std::vector<double>>& maps_ranges);
147 
148 private:
151 
154  };
155 } // namespace OpenMS
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
A container for features.
Definition: FeatureMap.h:80
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:49
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmTreeGuided.h:47
MapAlignmentAlgorithmTreeGuided(const MapAlignmentAlgorithmTreeGuided &)
Copy constructor intentionally not implemented -> private.
static void addPeptideSequences_(const std::vector< PeptideIdentification > &peptides, SeqAndRTList &peptide_rts, std::vector< double > &map_range, double feature_rt)
For given peptide identifications extract sequences and store with associated feature RT.
static void computeTransformedFeatureMaps(std::vector< FeatureMap > &feature_maps, const std::vector< TransformationDescription > &transformations)
Apply transformations on input maps.
String model_type_
Type of transformation model.
Definition: MapAlignmentAlgorithmTreeGuided.h:110
~MapAlignmentAlgorithmTreeGuided() override
Destructor.
static void buildTree(std::vector< FeatureMap > &feature_maps, std::vector< BinaryTreeNode > &tree, std::vector< std::vector< double >> &maps_ranges)
Extract RTs given for individual features of each map, calculate distances for each pair of maps and ...
Param model_param_
Default params of transformation models linear, b_spline, lowess and interpolated.
Definition: MapAlignmentAlgorithmTreeGuided.h:113
void computeTrafosByOriginalRT(std::vector< FeatureMap > &feature_maps, FeatureMap &map_transformed, std::vector< TransformationDescription > &transformations, const std::vector< Size > &trafo_order)
Extract original RT ("original_RT" MetaInfo) and transformed RT for each feature to compute RT transf...
MapAlignmentAlgorithmTreeGuided()
Default constructor.
void updateMembers_() override
This method is used to update extra member variables at the end of the setParameters() method.
void treeGuidedAlignment(const std::vector< BinaryTreeNode > &tree, std::vector< FeatureMap > &feature_maps_transformed, std::vector< std::vector< double >> &maps_ranges, FeatureMap &map_transformed, std::vector< Size > &trafo_order)
Align feature maps tree guided using align() of OpenMS::MapAlignmentAlgorithmIdentification and use T...
MapAlignmentAlgorithmTreeGuided & operator=(const MapAlignmentAlgorithmTreeGuided &)
Assignment operator intentionally not implemented -> private.
MapAlignmentAlgorithmIdentification align_algorithm_
Instantiation of alignment algorithm.
Definition: MapAlignmentAlgorithmTreeGuided.h:116
std::map< String, DoubleList > SeqAndRTList
Type to store feature retention times given for individual peptide sequence.
Definition: MapAlignmentAlgorithmTreeGuided.h:104
static void extractSeqAndRt_(const std::vector< FeatureMap > &feature_maps, std::vector< SeqAndRTList > &maps_seq_and_rt, std::vector< std::vector< double >> &maps_ranges)
For each input map, extract peptide identifications (sequences) of existing features with associated ...
void align(std::vector< FeatureMap > &data, std::vector< TransformationDescription > &transformations)
Align feature maps tree guided using align() of OpenMS::MapAlignmentAlgorithmIdentification and use T...
Management and storage of parameters / INI files.
Definition: Param.h:44
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:27
A more convenient string class.
Definition: String.h:34
Main OpenMS namespace.
Definition: openswathalgo/include/OpenMS/OPENSWATHALGO/DATAACCESS/ISpectrumAccess.h:19