89 static void buildTree(std::vector<FeatureMap>& feature_maps, std::vector<BinaryTreeNode>& tree, std::vector<std::vector<double>>& maps_ranges);
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);
112 void computeTrafosByOriginalRT(std::vector<FeatureMap>& feature_maps,
FeatureMap& map_transformed,
113 std::vector<TransformationDescription>& transformations,
const std::vector<Size>& trafo_order);
121 static void computeTransformedFeatureMaps(std::vector<FeatureMap>& feature_maps,
const std::vector<TransformationDescription>& transformations);
128 void updateMembers_()
override;
146 class PeptideIdentificationsPearsonDistance_;
156 static void addPeptideSequences_(
const std::vector<PeptideIdentification>& peptides,
SeqAndRTList& peptide_rts,
157 std::vector<double>& map_range,
double feature_rt);
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);
A more convenient string class.
Definition: String.h:58
A base class for all classes handling default parameters.
Definition: DefaultParamHandler.h:91
A container for features.
Definition: FeatureMap.h:95
Param model_param_
Default params of transformation models linear, b_spline, lowess and interpolated.
Definition: MapAlignmentAlgorithmTreeGuided.h:134
std::map< String, DoubleList > SeqAndRTList
Type to store feature retention times given for individual peptide sequence.
Definition: MapAlignmentAlgorithmTreeGuided.h:125
Main OpenMS namespace.
Definition: FeatureDeconvolution.h:46
Base class for all classes that want to report their progress.
Definition: ProgressLogger.h:54
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmIdentification.h:71
Management and storage of parameters / INI files.
Definition: Param.h:73
MapAlignmentAlgorithmIdentification align_algorithm_
Instantiation of alignment algorithm.
Definition: MapAlignmentAlgorithmTreeGuided.h:137
A map alignment algorithm based on peptide identifications from MS2 spectra.
Definition: MapAlignmentAlgorithmTreeGuided.h:71
String model_type_
Type of transformation model.
Definition: MapAlignmentAlgorithmTreeGuided.h:131