MRMFeatureFilter.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2018.
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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/FORMAT/TraMLFile.h>

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

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

namespace OpenMS
{

  class OPENMS_DLLAPI MRMFeatureFilter :
    public DefaultParamHandler
  {

public:

    MRMFeatureFilter();

    ~MRMFeatureFilter() override;

    void updateMembers_() override;

    void FilterFeatureMap(FeatureMap& features, const MRMFeatureQC& filter_criteria,
      const TargetedExperiment & transitions);
    
    void FeatureMapToAttachment(FeatureMap& features, QcMLFile::Attachment& attachment);
    
    double calculateIonRatio(const Feature & component_1, const Feature & component_2, const String & feature_name);
    
    double calculateRTDifference(Feature & component_1, Feature & component_2);
    
    double calculateResolution(Feature & component_1, Feature & component_2);

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

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

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

    // Members

    String flag_or_filter_;
    bool report_xic_;
    bool report_tic_;
    QcMLFile::Attachment attachment_;
    FeatureMap features_;
    std::map<String,std::vector<QcMLFile::QualityParameter>> component_group_qc_report_;
    std::map<String,std::vector<QcMLFile::QualityParameter>> component_qc_report_;
    std::map<std::vector<String>,std::vector<QcMLFile::QualityParameter>> multi_component_group_qc_report_;
  };
}