ConsensusMap.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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// $Maintainer: Timo Sachsenberg $
// $Authors: $
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#pragma once

#include <OpenMS/CONCEPT/UniqueIdInterface.h>
#include <OpenMS/CONCEPT/UniqueIdIndexer.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/KERNEL/ConsensusFeature.h>
#include <OpenMS/KERNEL/MSExperiment.h>

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

#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/CONCEPT/LogStream.h>
#include <OpenMS/DATASTRUCTURES/ExposedVector.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/DATASTRUCTURES/Utils/MapUtilities.h>
#include <OpenMS/OpenMSConfig.h>

#include <map>
#include <vector>
#include <iosfwd>

namespace OpenMS
{
  class PeptideIdentification;
  class PeptideHit;
  class ProteinIdentification;
  class DataProcessing;
  namespace Logger
  {
    class LogStream;
  }

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

    enum class SplitMeta
    {
      DISCARD,                
      COPY_ALL,               
      COPY_FIRST              
    };

    struct  ColumnHeader :
      public MetaInfoInterface
    {
      ColumnHeader() = default;

      ColumnHeader(const ColumnHeader&) = default;

      ColumnHeader& operator=(const ColumnHeader&) = default;

      String filename;

      String label;

      Size size = 0;

      UInt64 unique_id = UniqueIdInterface::INVALID;

      unsigned getLabelAsUInt(const String& experiment_type) const;
    };


    typedef ConsensusFeature FeatureType;
    typedef std::map<UInt64, ColumnHeader> ColumnHeaders;

    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;

    ConsensusMap();

    ConsensusMap(const ConsensusMap& source);
    ConsensusMap(ConsensusMap&& source);

    ~ConsensusMap() override;

    explicit ConsensusMap(size_type n);

    ConsensusMap& operator=(const ConsensusMap& source);
    ConsensusMap& operator=(ConsensusMap&& source) = default;

    ConsensusMap& appendRows(const ConsensusMap& rhs);

    ConsensusMap& appendColumns(const ConsensusMap& rhs);


    void clear(bool clear_meta_data = true);

    const ColumnHeaders& getColumnHeaders() const;

    ColumnHeaders& getColumnHeaders();

    void setColumnHeaders(const ColumnHeaders& column_description);

    const String& getExperimentType() const;

    void setExperimentType(const String& experiment_type);

    void sortByIntensity(bool reverse = false);

    void sortByRT();

    void sortByMZ();

    void sortByPosition();

    void sortByQuality(bool reverse = false);

    void sortBySize();

    void sortByMaps();

    void sortPeptideIdentificationsByMapIndex();

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

    void swap(ConsensusMap& from);

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

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

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

    void setProteinIdentifications(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;

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

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

    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).*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).*member_function)();
      }
      return assignments;
    }

    bool isMapConsistent(Logger::LogStream* stream = nullptr) const;

    std::vector<FeatureMap> split(SplitMeta mode = SplitMeta::DISCARD) const;


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

    const IdentificationData& getIdentificationData() const;

    IdentificationData& getIdentificationData();

  protected:
    ColumnHeaders column_description_;

    String experiment_type_ = "label-free";

    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 ConsensusMap& cons_map);

} // namespace OpenMS