OpenMS  3.0.0
MapAlignmentAlgorithmTreeGuided.h
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31 // $Maintainer: Julia Thueringer$
32 // $Authors: Julia Thueringer $
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34 
35 #pragma once
36 
41 
42 namespace OpenMS
43 {
70  class OPENMS_DLLAPI MapAlignmentAlgorithmTreeGuided :
71  public DefaultParamHandler,
72  public ProgressLogger
73  {
74 public:
77 
80 
88  static void buildTree(std::vector<FeatureMap>& feature_maps, std::vector<BinaryTreeNode>& tree, std::vector<std::vector<double>>& maps_ranges);
89 
99  void treeGuidedAlignment(const std::vector<BinaryTreeNode>& tree, std::vector<FeatureMap>& feature_maps_transformed,
100  std::vector<std::vector<double>>& maps_ranges, FeatureMap& map_transformed,
101  std::vector<Size>& trafo_order);
102 
106  void align(std::vector<FeatureMap>& data,
107  std::vector<TransformationDescription>& transformations);
108 
117  void computeTrafosByOriginalRT(std::vector<FeatureMap>& feature_maps, FeatureMap& map_transformed,
118  std::vector<TransformationDescription>& transformations, const std::vector<Size>& trafo_order);
119 
126  static void computeTransformedFeatureMaps(std::vector<FeatureMap>& feature_maps, const std::vector<TransformationDescription>& transformations);
127 
128 protected:
130  typedef std::map<String, DoubleList> SeqAndRTList;
131 
132  // Update defaults model_type_, model_param_ and align_algorithm_
133  void updateMembers_() override;
134 
137 
140 
143 
151  class PeptideIdentificationsPearsonDistance_;
152 
161  static void addPeptideSequences_(const std::vector<PeptideIdentification>& peptides, SeqAndRTList& peptide_rts,
162  std::vector<double>& map_range, double feature_rt);
163 
171  static void extractSeqAndRt_(const std::vector<FeatureMap>& feature_maps, std::vector<SeqAndRTList>& maps_seq_and_rt,
172  std::vector<std::vector<double>>& maps_ranges);
173 
174 private:
177 
180  };
181 } // namespace OpenMS
DefaultParamHandler.h
OpenMS::MapAlignmentAlgorithmTreeGuided::align_algorithm_
MapAlignmentAlgorithmIdentification align_algorithm_
Instantiation of alignment algorithm.
Definition: MapAlignmentAlgorithmTreeGuided.h:142
OpenMS::MapAlignmentAlgorithmTreeGuided::model_param_
Param model_param_
Default params of transformation models linear, b_spline, lowess and interpolated.
Definition: MapAlignmentAlgorithmTreeGuided.h:139
OpenMS::String
A more convenient string class.
Definition: String.h:58
BinaryTreeNode.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:92
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:47
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:52
ProgressLogger.h
OpenMS::MapAlignmentAlgorithmTreeGuided::SeqAndRTList
std::map< String, DoubleList > SeqAndRTList
Type to store feature retention times given for individual peptide sequence.
Definition: MapAlignmentAlgorithmTreeGuided.h:130
MapAlignmentAlgorithmIdentification.h
OpenMS::MapAlignmentAlgorithmIdentification
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:72
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:98
OpenMS::MapAlignmentAlgorithmTreeGuided
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmTreeGuided.h:70
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:69
OpenMS::MapAlignmentAlgorithmTreeGuided::model_type_
String model_type_
Type of transformation model.
Definition: MapAlignmentAlgorithmTreeGuided.h:136