MRMFeatureFilter.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 2002-2022.
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// $Maintainer: Douglas McCloskey, Pasquale Domenico Colaianni $
// $Authors: Douglas McCloskey, Pasquale Domenico Colaianni $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/ANALYSIS/OPENSWATH/MRMFeatureQC.h>
#include <OpenMS/ANALYSIS/TARGETED/TargetedExperiment.h>

#include <OpenMS/KERNEL/MRMFeature.h>
#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/FeatureMap.h>

#include <OpenMS/DATASTRUCTURES/DefaultParamHandler.h>
#include <OpenMS/DATASTRUCTURES/String.h>

namespace OpenMS
{
  class AbsoluteQuantitationMethod;

  class OPENMS_DLLAPI MRMFeatureFilter :
    public DefaultParamHandler
  {

public:

    MRMFeatureFilter();

    ~MRMFeatureFilter() override;

    void getDefaultParameters(Param& params) const;

    void updateMembers_() override;

    void FilterFeatureMap(FeatureMap& features, const MRMFeatureQC& filter_criteria,
      const TargetedExperiment& transitions);

    void FilterFeatureMapPercRSD(FeatureMap& features, const MRMFeatureQC& filter_criteria, const MRMFeatureQC& filter_values);

    void FilterFeatureMapBackgroundInterference(FeatureMap& features, const MRMFeatureQC& filter_criteria, const MRMFeatureQC& filter_values);

    void EstimateDefaultMRMFeatureQCValues(const std::vector<FeatureMap>& samples, MRMFeatureQC& filter_template, const TargetedExperiment& transitions, const bool& init_template_values) const;

    void TransferLLOQAndULOQToCalculatedConcentrationBounds(const std::vector<AbsoluteQuantitationMethod>& quantitation_method, MRMFeatureQC& filter_template);

    void EstimatePercRSD(const std::vector<FeatureMap>& samples, MRMFeatureQC& filter_template, const TargetedExperiment& transitions) const;

    void EstimateBackgroundInterferences(const std::vector<FeatureMap>& samples, MRMFeatureQC& filter_template, const TargetedExperiment& transitions) const;

    double calculateIonRatio(const Feature& component_1, const Feature& component_2, const String& feature_name) const;

    double calculateRTDifference(Feature& component_1, Feature& component_2) const;

    double calculateResolution(Feature& component_1, Feature& component_2) const;

    bool checkMetaValue(
      const Feature& component,
      const String& meta_value_key,
      const double& meta_value_l,
      const double& meta_value_u,
      bool& key_exists
    ) const;

    void updateMetaValue(
      const Feature& component,
      const String& meta_value_key,
      double& meta_value_l,
      double& meta_value_u,
      bool& key_exists
    ) const;

    void setMetaValue(
      const Feature& component,
      const String& meta_value_key,
      double& meta_value_l,
      double& meta_value_u,
      bool& key_exists
    ) const;

    void initMetaValue(
      const Feature& component,
      const String& meta_value_key,
      double& meta_value_l,
      double& meta_value_u,
      bool& key_exists
    ) const;

    std::map<String,int> countLabelsAndTransitionTypes(const Feature& component_group,
      const TargetedExperiment& transitions) const;

    StringList getUniqueSorted(const StringList& messages) const;

    void accumulateFilterValues(std::vector<MRMFeatureQC>& filter_values, const std::vector<FeatureMap>& samples, const MRMFeatureQC& filter_template, const TargetedExperiment& transitions) const;

    void zeroFilterValues(MRMFeatureQC& filter_zeros, const MRMFeatureQC& filter_template) const;

    void calculateFilterValuesMean(MRMFeatureQC& filter_mean, const std::vector<MRMFeatureQC>& filter_values, const MRMFeatureQC& filter_template) const;

    void calculateFilterValuesVar(MRMFeatureQC& filter_var, const std::vector<MRMFeatureQC>& filter_values, const MRMFeatureQC& filter_mean, const MRMFeatureQC& filter_template) const;

    void calculateFilterValuesPercRSD(MRMFeatureQC& filter_rsd, const MRMFeatureQC& filter_mean, const MRMFeatureQC& filter_var) const;

    template <typename T>
    bool checkRange(const T& value, const T& value_l, const T& value_u) const;

    template <typename T>
    void updateRange(const T& value, T& value_l, T& value_u) const;

    template <typename T>
    void setRange(const T& value, T& value_l, T& value_u) const;

    template <typename T>
    void initRange(const T& value, T& value_l, T& value_u) const;

private:
    // Members
    String flag_or_filter_;
  };
}