MetaboliteFeatureDeconvolution.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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// $Maintainer: Fabian Aicheler $
// $Authors: $
// --------------------------------------------------------------------------

#pragma once

// OpenMS
#include <OpenMS/KERNEL/FeatureMap.h>
#include <OpenMS/KERNEL/ConsensusMap.h>
#include <OpenMS/ANALYSIS/DECHARGING/ILPDCWrapper.h>
#include <OpenMS/DATASTRUCTURES/DPosition.h>
#include <OpenMS/DATASTRUCTURES/MassExplainer.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>

namespace OpenMS
{

  class Compomer;

  class OPENMS_DLLAPI MetaboliteFeatureDeconvolution :
    public DefaultParamHandler
  {
public:

    enum CHARGEMODE {QFROMFEATURE = 1, QHEURISTIC, QALL};

    typedef FeatureMap FeatureMapType;
    typedef Feature FeatureType;
    typedef DPosition<2> ClusterPointType;
    typedef FeatureMapType::FeatureType::CoordinateType CoordinateType;
    typedef ILPDCWrapper::PairsType PairsType;

    MetaboliteFeatureDeconvolution();

    MetaboliteFeatureDeconvolution(const MetaboliteFeatureDeconvolution& source);

    MetaboliteFeatureDeconvolution& operator=(const MetaboliteFeatureDeconvolution& source);

    ~MetaboliteFeatureDeconvolution() override;

    void compute(const FeatureMapType& fm_in, FeatureMapType& fm_out, ConsensusMap& cons_map, ConsensusMap& cons_map_p);


protected:


    void updateMembers_() override;

    struct CmpInfo_;

    /*
      @brief test for obviously wrong parameter settings and warn

      Currently supports the following scenarios:
      * If the lower charge bound is too high, consensus features with gapped, even charges will occur (e.g. 30,32,34), instead of the true (15,16,17)
      When more than 5% of the cf's look like this, we report it.

    */
    void checkSolution_(const ConsensusMap& cons_map) const;

    void inferMoreEdges_(PairsType& edges, Map<Size, std::set<CmpInfo_> >& feature_adducts);

    void candidateEdges_(FeatureMapType& fm_out, const Adduct& default_adduct, PairsType& feature_relation, Map<Size, std::set<CmpInfo_> >& feature_adducts);

    void annotate_feature_(FeatureMapType& fm_out, Adduct& default_adduct, Compomer& c, const Size f_idx, const UInt side, const Int new_q, const Int old_q);

    void printEdgesOfConnectedFeatures_(Size idx_1, Size idx_2, const PairsType& feature_relation);

    inline bool intensityFilterPassed_(const Int q1, const Int q2, const Compomer& cmp, const FeatureType& f1, const FeatureType& f2);

    bool chargeTestworthy_(const Int feature_charge, const Int putative_charge, const bool other_unchanged) const;

    MassExplainer::AdductsType potential_adducts_;
    Map<Size, String> map_label_;
    Map<String, Size> map_label_inverse_;
    bool enable_intensity_filter_;
    bool negative_mode_;
    CHARGEMODE q_try_;
    Int verbose_level_;

  };
} // namespace OpenMS