BaseFeature.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: Hendrik Weisser $
// $Authors: Hendrik Weisser, Chris Bielow $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/RichPeak2D.h>

namespace OpenMS
{

  class PeptideIdentification;

  class OPENMS_DLLAPI BaseFeature :
    public RichPeak2D
  {
public:

    typedef float QualityType;
    typedef Int ChargeType;
    typedef float WidthType;

    enum AnnotationState
    {
      FEATURE_ID_NONE,
      FEATURE_ID_SINGLE,
      FEATURE_ID_MULTIPLE_SAME,
      FEATURE_ID_MULTIPLE_DIVERGENT,
      SIZE_OF_ANNOTATIONSTATE
    };

    static const std::string NamesOfAnnotationState[SIZE_OF_ANNOTATIONSTATE];


    BaseFeature();

    BaseFeature(const BaseFeature& feature);

    explicit BaseFeature(const Peak2D& point);

    explicit BaseFeature(const RichPeak2D& point);

    ~BaseFeature() override;


    QualityType getQuality() const;
    void setQuality(QualityType q);
    struct QualityLess :
      std::binary_function<BaseFeature, BaseFeature, bool>
    {
      bool operator()(const BaseFeature& left, const BaseFeature& right) const
      {
        return left.getQuality() < right.getQuality();
      }

      bool operator()(const BaseFeature& left, const QualityType& right) const
      {
        return left.getQuality() < right;
      }

      bool operator()(const QualityType& left, const BaseFeature& right) const
      {
        return left < right.getQuality();
      }

      bool operator()(const QualityType& left, const QualityType& right) const
      {
        return left < right;
      }

    };

    WidthType getWidth() const;
    void setWidth(WidthType fwhm);

    const ChargeType& getCharge() const;

    void setCharge(const ChargeType& ch);

    BaseFeature& operator=(const BaseFeature& rhs);

    bool operator==(const BaseFeature& rhs) const;

    bool operator!=(const BaseFeature& rhs) const;

    const std::vector<PeptideIdentification>& getPeptideIdentifications() const;

    std::vector<PeptideIdentification>& getPeptideIdentifications();

    void setPeptideIdentifications(const std::vector<PeptideIdentification>& peptides);

    AnnotationState getAnnotationState() const;

protected:

    QualityType quality_;

    ChargeType charge_;

    WidthType width_;

    std::vector<PeptideIdentification> peptides_;
  };

} // namespace OpenMS