MapAlignmentAlgorithmTreeGuided.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// $Maintainer: Julia Thueringer$
// $Authors: Julia Thueringer $
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#pragma once

#include <OpenMS/CONCEPT/ProgressLogger.h>
#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/BinaryTreeNode.h>
#include <OpenMS/ANALYSIS/MAPMATCHING/MapAlignmentAlgorithmIdentification.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MapAlignmentAlgorithmTreeGuided :
    public DefaultParamHandler,
    public ProgressLogger
  {
public:
    MapAlignmentAlgorithmTreeGuided();

    ~MapAlignmentAlgorithmTreeGuided() override;

    static void buildTree(std::vector<FeatureMap>& feature_maps, std::vector<BinaryTreeNode>& tree, std::vector<std::vector<double>>& maps_ranges);

    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);

    void align(std::vector<FeatureMap>& data,
               std::vector<TransformationDescription>& transformations);

    void computeTrafosByOriginalRT(std::vector<FeatureMap>& feature_maps, FeatureMap& map_transformed,
                                   std::vector<TransformationDescription>& transformations, const std::vector<Size>& trafo_order);

    static void computeTransformedFeatureMaps(std::vector<FeatureMap>& feature_maps, const std::vector<TransformationDescription>& transformations);

protected:
    typedef std::map<String, DoubleList> SeqAndRTList;

    // Update defaults model_type_, model_param_ and align_algorithm_
    void updateMembers_() override;

    String model_type_;

    Param model_param_;

    MapAlignmentAlgorithmIdentification align_algorithm_;

    class PeptideIdentificationsPearsonDistance_;

    static void addPeptideSequences_(const std::vector<PeptideIdentification>& peptides, SeqAndRTList& peptide_rts,
            std::vector<double>& map_range, double feature_rt);

    static void extractSeqAndRt_(const std::vector<FeatureMap>& feature_maps, std::vector<SeqAndRTList>& maps_seq_and_rt,
            std::vector<std::vector<double>>& maps_ranges);

private:
    MapAlignmentAlgorithmTreeGuided(const MapAlignmentAlgorithmTreeGuided&);

    MapAlignmentAlgorithmTreeGuided& operator=(const MapAlignmentAlgorithmTreeGuided&);
  };
} // namespace OpenMS