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/Utils/MapUtilities.h>

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

#include <exception>
#include <vector>

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 FeatureMap :
    private std::vector<Feature>,
    public MetaInfoInterface,
    public RangeManagerContainer<RangeRT, RangeMZ, RangeIntensity>,
    public DocumentIdentifier,
    public UniqueIdInterface,
    public UniqueIdIndexer<FeatureMap>,
    public MapUtilities<FeatureMap>
  {
public:
    typedef std::vector<Feature> Base;

    // types
    using Base::value_type;
    using Base::iterator;
    using Base::const_iterator;
    using Base::size_type;
    using Base::pointer; // ConstRefVector
    using Base::reference; // ConstRefVector
    using Base::const_reference; // ConstRefVector
    using Base::difference_type; // ConstRefVector

    // functions
    using Base::begin;
    using Base::end;
    using Base::cbegin;
    using Base::cend;
    using Base::size;
    using Base::resize; // ConsensusMap, FeatureXMLFile
    using Base::empty;
    using Base::reserve;
    using Base::operator[];
    using Base::at; // UniqueIdIndexer
    using Base::back; // FeatureXMLFile

    using Base::push_back;
    using Base::emplace_back;
    using Base::pop_back; // FeatureXMLFile
    using Base::erase; // source/VISUAL/Plot2DCanvas.cpp 2871, FeatureMap_test 599

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


    OPENMS_DLLAPI FeatureMap();

    OPENMS_DLLAPI FeatureMap(const FeatureMap& source);

    OPENMS_DLLAPI FeatureMap(FeatureMap&& source);

    OPENMS_DLLAPI ~FeatureMap() override;

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

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

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

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

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

    OPENMS_DLLAPI void sortByIntensity(bool reverse = false);

    OPENMS_DLLAPI void sortByPosition();

    OPENMS_DLLAPI void sortByRT();

    OPENMS_DLLAPI void sortByMZ();

    OPENMS_DLLAPI void sortByOverallQuality(bool reverse = false);


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

    OPENMS_DLLAPI void swapFeaturesOnly(FeatureMap& from);

    OPENMS_DLLAPI void swap(FeatureMap& from);

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

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

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

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

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

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

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

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

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

    OPENMS_DLLAPI void setPrimaryMSRunPath(const StringList& s);

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

    OPENMS_DLLAPI void getPrimaryMSRunPath(StringList& toFill) const;

    OPENMS_DLLAPI 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;
    }

    OPENMS_DLLAPI AnnotationStatistics getAnnotationStatistics() const;


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

    OPENMS_DLLAPI const IdentificationData& getIdentificationData() const;

    OPENMS_DLLAPI 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