FeatureMap.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2022.
//
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//    may be used to endorse or promote products derived from this software
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// $Maintainer: Chris Bielow $
// $Authors: Marc Sturm, Chris Bielow, Clemens Groepl $
// --------------------------------------------------------------------------

#pragma once

#include <OpenMS/KERNEL/Feature.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/KERNEL/MSExperiment.h>

#include <OpenMS/METADATA/DocumentIdentifier.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
#include <OpenMS/METADATA/ID/Observation.h>

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/UniqueIdInterface.h>
#include <OpenMS/CONCEPT/UniqueIdIndexer.h>
#include <OpenMS/DATASTRUCTURES/ExposedVector.h>
#include <OpenMS/DATASTRUCTURES/Utils/MapUtilities.h>

#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/OpenMSConfig.h>

#include <exception>

namespace OpenMS
{
  class ProteinIdentification;
  class PeptideIdentification;
  class DataProcessing;

  struct OPENMS_DLLAPI AnnotationStatistics
  {
    std::vector<Size> states; 

    AnnotationStatistics();

    AnnotationStatistics(const AnnotationStatistics& rhs);

    AnnotationStatistics& operator=(const AnnotationStatistics& rhs);

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

    AnnotationStatistics& operator+=(BaseFeature::AnnotationState state);
  };


  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const AnnotationStatistics& ann);

  class OPENMS_DLLAPI FeatureMap :
      public MetaInfoInterface,
      public RangeManagerContainer<RangeRT, RangeMZ, RangeIntensity>,
      public DocumentIdentifier,
      public ExposedVector<Feature>,
      public UniqueIdInterface,
      public UniqueIdIndexer<FeatureMap>,
      public MapUtilities<FeatureMap>
  {
  public:
    EXPOSED_VECTOR_INTERFACE(Feature)

    //@{
    typedef RangeManagerContainer<RangeRT, RangeMZ, RangeIntensity> RangeManagerContainerType;
    typedef RangeManager<RangeRT, RangeMZ, RangeIntensity> RangeManagerType;
    typedef iterator Iterator;
    typedef const_iterator ConstIterator;
    typedef reverse_iterator ReverseIterator;
    typedef const_reverse_iterator ConstReverseIterator;


    FeatureMap();

    FeatureMap(const FeatureMap& source);

    FeatureMap(FeatureMap&& source);

    FeatureMap& operator=(const FeatureMap& rhs);

    //FeatureMap& FeatureMap::operator=(FeatureMap&&);

    ~FeatureMap() override;

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

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

    FeatureMap operator+(const FeatureMap& rhs) const;

    FeatureMap& operator+=(const FeatureMap& rhs);

    void sortByIntensity(bool reverse = false);

    void sortByPosition();

    void sortByRT();

    void sortByMZ();

    void sortByOverallQuality(bool reverse = false);


    // Docu in base class
    void updateRanges() override;

    void swapFeaturesOnly(FeatureMap& from);

    void swap(FeatureMap& from);

    const std::vector<ProteinIdentification>& getProteinIdentifications() const;

    std::vector<ProteinIdentification>& getProteinIdentifications();

    void setProteinIdentifications(const std::vector<ProteinIdentification>& protein_identifications);

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

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

    void setUnassignedPeptideIdentifications(const std::vector<PeptideIdentification>& unassigned_peptide_identifications);

    const std::vector<DataProcessing>& getDataProcessing() const;

    std::vector<DataProcessing>& getDataProcessing();

    void setDataProcessing(const std::vector<DataProcessing>& processing_method);

    void setPrimaryMSRunPath(const StringList& s);

    void setPrimaryMSRunPath(const StringList& s, MSExperiment & e);

    void getPrimaryMSRunPath(StringList& toFill) const;

    void clear(bool clear_meta_data = true);

    template <typename Type>
    Size applyMemberFunction(Size (Type::* member_function)())
    {
      Size assignments = 0;
      assignments += ((*this).*member_function)();
      for (Iterator iter = this->begin(); iter != this->end(); ++iter)
      {
        assignments += iter->applyMemberFunction(member_function);
      }
      return assignments;
    }

    template <typename Type>
    Size applyMemberFunction(Size (Type::* member_function)() const) const
    {
      Size assignments = 0;
      assignments += ((*this).*member_function)();
      for (ConstIterator iter = this->begin(); iter != this->end(); ++iter)
      {
        assignments += iter->applyMemberFunction(member_function);
      }
      return assignments;
    }

    AnnotationStatistics getAnnotationStatistics() const;


    std::set<IdentificationData::ObservationMatchRef> getUnassignedIDMatches() const;

    const IdentificationData& getIdentificationData() const;

    IdentificationData& getIdentificationData();

protected:
    std::vector<ProteinIdentification> protein_identifications_;

    std::vector<PeptideIdentification> unassigned_peptide_identifications_;

    std::vector<DataProcessing> data_processing_;

    IdentificationData id_data_;
  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const FeatureMap& map);

} // namespace OpenMS