BaseFeature.h

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// Copyright (c) 2002-present, The OpenMS Team -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Hendrik Weisser $
// $Authors: Hendrik Weisser, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/RichPeak2D.h>
#include <OpenMS/METADATA/PeptideIdentification.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
 
#include <optional>
 
namespace OpenMS
{
  class FeatureHandle;
 
  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) = default;
 
    BaseFeature(BaseFeature&& feature) noexcept
      : RichPeak2D(std::move(feature))
    {
      quality_ = feature.quality_;
      charge_ = feature.charge_;
      width_ = feature.width_;
      // Note: will terminate program if move assignment throws because of noexcept
      // but we can't recover in that case anyways and we need to mark it noexcept for the move.
      peptides_ = std::move(feature.peptides_);
      primary_id_ = std::move(feature.primary_id_);
      id_matches_ = std::move(feature.id_matches_);
    }
 
    BaseFeature(const BaseFeature& rhs, UInt64 map_index);
 
    explicit BaseFeature(const Peak2D& point);
 
    explicit BaseFeature(const RichPeak2D& point);
 
    explicit BaseFeature(const FeatureHandle& fh);
 
    ~BaseFeature() override;
 
    QualityType getQuality() const;
    void setQuality(QualityType q);
    struct QualityLess
    {
      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) = default;
 
    BaseFeature& operator=(BaseFeature&& rhs) & = default;
 
    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);
 
    void sortPeptideIdentifications();
 
    AnnotationState getAnnotationState() const;
 
    bool hasPrimaryID() const;
 
    const IdentificationData::IdentifiedMolecule& getPrimaryID() const;
 
    void clearPrimaryID();
 
    void setPrimaryID(const IdentificationData::IdentifiedMolecule& id);
 
    const std::set<IdentificationData::ObservationMatchRef>& getIDMatches() const;
 
    std::set<IdentificationData::ObservationMatchRef>& getIDMatches();
 
    void addIDMatch(IdentificationData::ObservationMatchRef ref);
 
    void updateIDReferences(const IdentificationData::RefTranslator& trans);
 
protected:
 
    QualityType quality_;
 
    ChargeType charge_;
 
    WidthType width_;
 
    std::vector<PeptideIdentification> peptides_;
 
    std::optional<IdentificationData::IdentifiedMolecule> primary_id_;
 
    std::set<IdentificationData::ObservationMatchRef> id_matches_;
  };
 
} // namespace OpenMS