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 2002-2021.
//
// This software is released under a three-clause BSD license:
//  * Redistributions of source code must retain the above copyright
//    notice, this list of conditions and the following disclaimer.
//  * Redistributions in binary form must reproduce the above copyright
//    notice, this list of conditions and the following disclaimer in the
//    documentation and/or other materials provided with the distribution.
//  * Neither the name of any author or any participating institution
//    may be used to endorse or promote products derived from this software
//    without specific prior written permission.
// For a full list of authors, refer to the file AUTHORS.
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// THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
// AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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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::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