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 2002-2018.
//
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//    may be used to endorse or promote products derived from this software
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// $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/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OpenMSConfig.h>

#include <map>
#include <vector>

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

  class ConsensusMap : // no OPENMS_DLLAPI here, since the class is derived from an STL class - we do not want parts of the STL lib in OpenMS.lib, since it will cause linker errors
    private std::vector<ConsensusFeature>,
    public MetaInfoInterface,
    public RangeManager<2>,
    public DocumentIdentifier,
    public UniqueIdInterface,
    public UniqueIdIndexer<ConsensusMap>
  {

public:
    typedef std::vector<ConsensusFeature> privvec;

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

    // functions
    using privvec::begin;
    using privvec::end;

    using privvec::size;
    using privvec::resize;
    using privvec::empty;
    using privvec::reserve;
    using privvec::operator[];
    using privvec::at; // UniqueIdIndexer
    using privvec::back; // source/ANALYSIS/DECHARGING/FeatureDeconvolution.cpp:977:

    using privvec::push_back;

    struct OPENMS_DLLAPI ColumnHeader :
      public MetaInfoInterface
    {
      ColumnHeader();

      ColumnHeader(const ColumnHeader&);

      String filename;
      String label;
      Size size;
      UInt64 unique_id;
    };


    typedef std::vector<ConsensusFeature> Base;
    typedef RangeManager<2> RangeManagerType;
    typedef std::map<UInt64, ColumnHeader> ColumnHeaders;
    typedef std::vector<ConsensusFeature>::iterator Iterator;
    typedef std::vector<ConsensusFeature>::const_iterator ConstIterator;
    typedef std::vector<ConsensusFeature>::reverse_iterator ReverseIterator;
    typedef std::vector<ConsensusFeature>::const_reverse_iterator ConstReverseIterator;

    OPENMS_DLLAPI ConsensusMap();

    OPENMS_DLLAPI ConsensusMap(const ConsensusMap& source);

    OPENMS_DLLAPI ~ConsensusMap() override;

    OPENMS_DLLAPI explicit ConsensusMap(Base::size_type n);

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

    OPENMS_DLLAPI ConsensusMap& appendRows(const ConsensusMap& rhs);

    OPENMS_DLLAPI ConsensusMap& appendColumns(const ConsensusMap& rhs);


    OPENMS_DLLAPI void clear(bool clear_meta_data = true);

    OPENMS_DLLAPI const ColumnHeaders& getColumnHeaders() const;

    OPENMS_DLLAPI ColumnHeaders& getColumnHeaders();

    OPENMS_DLLAPI void setColumnHeaders(const ColumnHeaders& column_description);

    OPENMS_DLLAPI const String& getExperimentType() const;

    OPENMS_DLLAPI void setExperimentType(const String& experiment_type);

    OPENMS_DLLAPI void sortByIntensity(bool reverse = false);

    OPENMS_DLLAPI void sortByRT();

    OPENMS_DLLAPI void sortByMZ();

    OPENMS_DLLAPI void sortByPosition();

    OPENMS_DLLAPI void sortByQuality(bool reverse = false);

    OPENMS_DLLAPI void sortBySize();

    OPENMS_DLLAPI void sortByMaps();

    OPENMS_DLLAPI void sortPeptideIdentificationsByMapIndex();

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

    OPENMS_DLLAPI void swap(ConsensusMap& 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 getPrimaryMSRunPath(StringList& toFill) const;

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

    OPENMS_DLLAPI 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;

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_;
  };

  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusMap& cons_map);

} // namespace OpenMS