MRMFeature.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: Hannes Roest $
// $Authors: Hannes Roest $
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#pragma once

#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/ANALYSIS/OPENSWATH/OpenSwathScores.h>

namespace OpenMS
{
  class OPENMS_DLLAPI MRMFeature :
    public Feature
  {
public:


    typedef std::vector<Feature> FeatureListType;


    MRMFeature();

    MRMFeature(const MRMFeature &rhs);

    MRMFeature(MRMFeature &&rhs) = default;

    MRMFeature & operator=(const MRMFeature & rhs);

    MRMFeature& operator=(MRMFeature&&) & = default;

    ~MRMFeature() override;



    const OpenSwath_Scores & getScores() const;

    OpenSwath_Scores & getScores();

    Feature & getFeature(const String& key);

    const Feature & getFeature(const String& key) const;

    void setScores(const OpenSwath_Scores & scores);

    void addScore(const String & score_name, double score);

    void addFeature(const Feature & feature, const String& key);

    void addFeature(Feature && feature, const String& key);

    const std::vector<Feature> & getFeatures() const;

    void getFeatureIDs(std::vector<String> & result) const;

    void addPrecursorFeature(const Feature & feature, const String& key);

    void addPrecursorFeature(Feature && feature, const String& key);

    void getPrecursorFeatureIDs(std::vector<String> & result) const;

    Feature & getPrecursorFeature(const String& key);

    const Feature & getPrecursorFeature(const String& key) const;

    void IDScoresAsMetaValue(bool decoy, const OpenSwath_Ind_Scores& idscores);

protected:

    FeatureListType features_;

    FeatureListType precursor_features_;

    OpenSwath_Scores pg_scores_;

    std::map<String, int> feature_map_;

    std::map<String, int> precursor_feature_map_;

  };
}