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MapAlignmentAlgorithmTreeGuided.h
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1 // Copyright (c) 2002-present, OpenMS Inc. -- 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 
16 
17 namespace OpenMS
18 {
45  class OPENMS_DLLAPI MapAlignmentAlgorithmTreeGuided :
46  public DefaultParamHandler,
47  public ProgressLogger
48  {
49 public:
52 
55 
63  static void buildTree(std::vector<FeatureMap>& feature_maps, std::vector<BinaryTreeNode>& tree, std::vector<std::vector<double>>& maps_ranges);
64 
74  void treeGuidedAlignment(const std::vector<BinaryTreeNode>& tree, std::vector<FeatureMap>& feature_maps_transformed,
75  std::vector<std::vector<double>>& maps_ranges, FeatureMap& map_transformed,
76  std::vector<Size>& trafo_order);
77 
81  void align(std::vector<FeatureMap>& data,
82  std::vector<TransformationDescription>& transformations);
83 
92  void computeTrafosByOriginalRT(std::vector<FeatureMap>& feature_maps, FeatureMap& map_transformed,
93  std::vector<TransformationDescription>& transformations, const std::vector<Size>& trafo_order);
94 
101  static void computeTransformedFeatureMaps(std::vector<FeatureMap>& feature_maps, const std::vector<TransformationDescription>& transformations);
102 
103 protected:
105  typedef std::map<String, DoubleList> SeqAndRTList;
106 
107  // Update defaults model_type_, model_param_ and align_algorithm_
108  void updateMembers_() override;
109 
112 
115 
118 
126  class PeptideIdentificationsPearsonDistance_;
127 
136  static void addPeptideSequences_(const PeptideIdentificationList& peptides, SeqAndRTList& peptide_rts,
137  std::vector<double>& map_range, double feature_rt);
138 
146  static void extractSeqAndRt_(const std::vector<FeatureMap>& feature_maps, std::vector<SeqAndRTList>& maps_seq_and_rt,
147  std::vector<std::vector<double>>& maps_ranges);
148 
149 private:
152 
155  };
156 } // namespace OpenMS
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:66
A container for features.
Definition: FeatureMap.h:82
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:56
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmTreeGuided.h:48
MapAlignmentAlgorithmTreeGuided(const MapAlignmentAlgorithmTreeGuided &)
Copy constructor intentionally not implemented -> private.
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:111
~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:114
static void addPeptideSequences_(const PeptideIdentificationList &peptides, SeqAndRTList &peptide_rts, std::vector< double > &map_range, double feature_rt)
For given peptide identifications extract sequences and store with associated feature RT.
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:117
std::map< String, DoubleList > SeqAndRTList
Type to store feature retention times given for individual peptide sequence.
Definition: MapAlignmentAlgorithmTreeGuided.h:105
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
Container for peptide identifications from multiple spectra.
Definition: PeptideIdentificationList.h:66
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