BaseFeature.h

Go to the documentation of this file.

// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
// --------------------------------------------------------------------------
// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
// IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
// ARE DISCLAIMED. IN NO EVENT SHALL ANY OF THE AUTHORS OR THE CONTRIBUTING
// INSTITUTIONS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL,
// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
// PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS;
// OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY,
// WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR
// OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF
// ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
//
// --------------------------------------------------------------------------
// $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