MRMFeatureSelector.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
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//    may be used to endorse or promote products derived from this software
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// For a full list of authors, refer to the file AUTHORS.
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// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni, Svetlana Kutuzova $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni, Svetlana Kutuzova $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/config.h> // OPENMS_DLLAPI
#include <OpenMS/DATASTRUCTURES/LPWrapper.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/KERNEL/FeatureMap.h>

namespace OpenMS
{

  class OPENMS_DLLAPI MRMFeatureSelector
  {
public:
    MRMFeatureSelector() = default;
    virtual ~MRMFeatureSelector() = default;

    enum class VariableType
    {
      INTEGER = 1,
      CONTINUOUS
    };

    enum class LambdaScore
    {
      LINEAR = 1,
      INVERSE,
      LOG,
      INVERSE_LOG,
      INVERSE_LOG10
    };

    friend class MRMFeatureSelector_test;

    struct SelectorParameters
    {
      SelectorParameters() = default;

      SelectorParameters(
        Int nn,
        bool lw,
        bool stg,
        Int swl,
        Int ssl,
        MRMFeatureSelector::VariableType vt,
        double ot,
        std::map<String, MRMFeatureSelector::LambdaScore>& sw
      ) :
        nn_threshold(nn),
        locality_weight(lw),
        select_transition_group(stg),
        segment_window_length(swl),
        segment_step_length(ssl),
        variable_type(vt),
        optimal_threshold(ot),
        score_weights(sw) {}

      Int    nn_threshold            = 4; 
      bool   locality_weight         = false; 
      bool   select_transition_group = true; 
      Int    segment_window_length   = 8; 
      Int    segment_step_length     = 4; 
      MRMFeatureSelector::VariableType variable_type = MRMFeatureSelector::VariableType::CONTINUOUS; 
      double optimal_threshold       = 0.5; 
      std::map<String, MRMFeatureSelector::LambdaScore> score_weights; 
    };

    virtual void optimize(
      const std::vector<std::pair<double, String>>& time_to_name,
      const std::map<String, std::vector<Feature>>& feature_name_map,
      std::vector<String>& result,
      const SelectorParameters& parameters
    ) const = 0;

    void selectMRMFeature(
      const FeatureMap& features,
      FeatureMap& selected_filtered,
      const SelectorParameters& parameters
    ) const;

protected:
    Int addVariable_(
      LPWrapper& problem,
      const String& name,
      const bool bounded,
      const double obj,
      const VariableType variableType
    ) const;

    double computeScore_(const Feature& feature, const std::map<String, LambdaScore>& score_weights) const;

    void addConstraint_(
      LPWrapper& problem,
      const std::vector<Int>& indices,
      const std::vector<double>& values,
      const String& name,
      const double lb,
      const double ub,
      const LPWrapper::Type param
    ) const;

private:
    void constructTargTransList_(
      const FeatureMap& features,
      std::vector<std::pair<double, String>>& time_to_name,
      std::map<String, std::vector<Feature>>& feature_name_map,
      const bool select_transition_group
    ) const;

    double weightScore_(const double score, const LambdaScore lambda_score) const;

    String removeSpaces_(String str) const;
  };

  class OPENMS_DLLAPI MRMFeatureSelectorQMIP : public MRMFeatureSelector
  {
public:
    void optimize(
      const std::vector<std::pair<double, String>>& time_to_name,
      const std::map<String, std::vector<Feature>>& feature_name_map,
      std::vector<String>& result,
      const SelectorParameters& parameters
    ) const override;
  };

  class OPENMS_DLLAPI MRMFeatureSelectorScore : public MRMFeatureSelector
  {
public:
    void optimize(
      const std::vector<std::pair<double, String>>& time_to_name,
      const std::map<String, std::vector<Feature>>& feature_name_map,
      std::vector<String>& result,
      const SelectorParameters& parameters
    ) const override;
  };

  class MRMFeatureSelector_test : public MRMFeatureSelectorQMIP
  {
public:
    MRMFeatureSelector_test() = default;
    ~MRMFeatureSelector_test() override = default;

    void constructTargTransList_(
      const FeatureMap& features,
      std::vector<std::pair<double, String>>& time_to_name,
      std::map<String, std::vector<Feature>>& feature_name_map,
      const bool select_transition_group
    ) const
    {
      selector_.constructTargTransList_(features, time_to_name, feature_name_map, select_transition_group);
    }

    double weightScore_(const double score, const LambdaScore lambda_score) const
    {
      return selector_.weightScore_(score, lambda_score);
    }

    double computeScore_(const Feature& feature, const std::map<String, LambdaScore>& score_weights) const
    {
      return selector_.computeScore_(feature, score_weights);
    }

    String removeSpaces_(String str) const
    {
      return selector_.removeSpaces_(str);
    }

    MRMFeatureSelectorQMIP selector_;
  };
}