ConsensusMap.h

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// Copyright (c) 2002-present, OpenMS Inc. -- EKU Tuebingen, ETH Zurich, and FU Berlin
// SPDX-License-Identifier: BSD-3-Clause
//
// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/CONCEPT/UniqueIdInterface.h>
#include <OpenMS/CONCEPT/UniqueIdIndexer.h>
#include <OpenMS/KERNEL/RangeManager.h>
#include <OpenMS/KERNEL/ConsensusFeature.h>
 
#include <OpenMS/METADATA/DocumentIdentifier.h>
#include <OpenMS/METADATA/MetaInfoInterface.h>
#include <OpenMS/METADATA/PeptideIdentificationList.h>
#include <OpenMS/METADATA/ProteinIdentification.h>
#include <OpenMS/METADATA/ID/IdentificationData.h>
 
#include <OpenMS/CONCEPT/Types.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;
  class MSExperiment;
  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 OPENMS_DLLAPI 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 ProteinIdentification* findProteinIdentification(const String& identifier) const;
 
    ProteinIdentification* findProteinIdentification(const String& identifier);
 
    const PeptideIdentificationList& getUnassignedPeptideIdentifications() const;
 
    PeptideIdentificationList& getUnassignedPeptideIdentifications();
 
    void setUnassignedPeptideIdentifications(const PeptideIdentificationList& 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_;
 
    PeptideIdentificationList 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