| OpenMS 2.5.0

MapAlignmentAlgorithmTreeGuided.h
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2 // OpenMS -- Open-Source Mass Spectrometry
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30 // --------------------------------------------------------------------------
31 // $Maintainer: Julia Thueringer$
32 // $Authors: Julia Thueringer $
33 // --------------------------------------------------------------------------
34
35 #pragma once
36
37 #include <OpenMS/CONCEPT/ProgressLogger.h>
38 #include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
39 #include <OpenMS/DATASTRUCTURES/BinaryTreeNode.h>
40 #include <OpenMS/APPLICATIONS/MapAlignerBase.h>
41 #include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmIdentification.h>
42
43 namespace OpenMS
44 {
71 class OPENMS_DLLAPI MapAlignmentAlgorithmTreeGuided :
72 public DefaultParamHandler,
73 public ProgressLogger
74 {
75 public:
77 MapAlignmentAlgorithmTreeGuided();
78
80 ~MapAlignmentAlgorithmTreeGuided() override;
81
89 static void buildTree(std::vector<FeatureMap>& feature_maps, std::vector<BinaryTreeNode>& tree, std::vector<std::vector<double>>& maps_ranges);
90
100 void treeGuidedAlignment(const std::vector<BinaryTreeNode>& tree, std::vector<FeatureMap> feature_maps_transformed,
101 std::vector<std::vector<double>>& maps_ranges, FeatureMap& map_transformed,
102 std::vector<Size>& trafo_order);
103
112 void computeTrafosByOriginalRT(std::vector<FeatureMap>& feature_maps, FeatureMap& map_transformed,
113 std::vector<TransformationDescription>& transformations, const std::vector<Size>& trafo_order);
114
121 static void computeTransformedFeatureMaps(std::vector<FeatureMap>& feature_maps, const std::vector<TransformationDescription>& transformations);
122
123 protected:
125 typedef std::map<String, DoubleList> SeqAndRTList;
126
127 // Update defaults model_type_, model_param_ and align_algorithm_
128 void updateMembers_() override;
129
131 String model_type_;
132
134 Param model_param_;
135
137 MapAlignmentAlgorithmIdentification align_algorithm_;
138
146 class PeptideIdentificationsPearsonDistance_;
147
156 static void addPeptideSequences_(const std::vector<PeptideIdentification>& peptides, SeqAndRTList& peptide_rts,
157 std::vector<double>& map_range, double feature_rt);
158
166 static void extractSeqAndRt_(const std::vector<FeatureMap>& feature_maps, std::vector<SeqAndRTList>& maps_seq_and_rt,
167 std::vector<std::vector<double>>& maps_ranges);
168
169 private:
171 MapAlignmentAlgorithmTreeGuided(const MapAlignmentAlgorithmTreeGuided&);
172
174 MapAlignmentAlgorithmTreeGuided& operator=(const MapAlignmentAlgorithmTreeGuided&);
175 };
176 } // namespace OpenMS
OpenMS::String
A more convenient string class.
Definition: String.h:58
MapAlignerBase.h
OpenMS::DefaultParamHandler
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
BinaryTreeNode.h
OpenMS::FeatureMap
A container for features.
Definition: FeatureMap.h:95
OpenMS::MapAlignmentAlgorithmTreeGuided::model_param_
Param model_param_
Default params of transformation models linear, b_spline, lowess and interpolated.
Definition: MapAlignmentAlgorithmTreeGuided.h:134
OpenMS::MapAlignmentAlgorithmTreeGuided::SeqAndRTList
std::map< String, DoubleList > SeqAndRTList
Type to store feature retention times given for individual peptide sequence.
Definition: MapAlignmentAlgorithmTreeGuided.h:125
MapAlignmentAlgorithmIdentification.h
ProgressLogger.h
OpenMS
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
OpenMS::ProgressLogger
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
DefaultParamHandler.h
OpenMS::MapAlignmentAlgorithmIdentification
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:71
OpenMS::Param
Management and storage of parameters / INI files.
Definition: Param.h:73
OpenMS::MapAlignmentAlgorithmTreeGuided::align_algorithm_
MapAlignmentAlgorithmIdentification align_algorithm_
Instantiation of alignment algorithm.
Definition: MapAlignmentAlgorithmTreeGuided.h:137
OpenMS::MapAlignmentAlgorithmTreeGuided
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmTreeGuided.h:71
OpenMS::MapAlignmentAlgorithmTreeGuided::model_type_
String model_type_
Type of transformation model.
Definition: MapAlignmentAlgorithmTreeGuided.h:131