ConsensusFeature.h

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// --------------------------------------------------------------------------
//                   OpenMS -- Open-Source Mass Spectrometry
// --------------------------------------------------------------------------
// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
//
// 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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// EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO,
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// --------------------------------------------------------------------------
// $Maintainer: Timo Sachsenberg $
// $Authors: $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/DATASTRUCTURES/DRange.h>
#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/FeatureHandle.h>
 
#include <OpenMS/CONCEPT/Types.h>
#include <OpenMS/DATASTRUCTURES/String.h>
#include <OpenMS/OpenMSConfig.h>
 
#include <set>
 
namespace OpenMS
{
  class FeatureMap;
  class Peak2D;
 
  class OPENMS_DLLAPI ConsensusFeature :
    public BaseFeature
  {
public:
 
    typedef std::set<FeatureHandle, FeatureHandle::IndexLess> HandleSetType;
    typedef HandleSetType::const_iterator const_iterator;
    typedef HandleSetType::iterator iterator;
    typedef HandleSetType::const_reverse_iterator const_reverse_iterator;
    typedef HandleSetType::reverse_iterator reverse_iterator;
 
    struct SizeLess
    {
      inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
      {
        return left.size() < right.size();
      }
 
      inline bool operator()(ConsensusFeature const& left, UInt64 const& right) const
      {
        return left.size() < right;
      }
 
      inline bool operator()(UInt64 const& left, ConsensusFeature const& right) const
      {
        return left < right.size();
      }
 
      inline bool operator()(const UInt64& left, const UInt64& right) const
      {
        return left < right;
      }
 
    };
 
    struct MapsLess
    {
      inline bool operator()(ConsensusFeature const& left, ConsensusFeature const& right) const
      {
        return std::lexicographical_compare(left.begin(), left.end(), right.begin(), right.end(), FeatureHandle::IndexLess());
      }
 
    };
 
    struct Ratio
    {
      Ratio()
      {
      }
 
      Ratio(const Ratio& rhs)
      {
        ratio_value_ = rhs.ratio_value_;
        denominator_ref_ = rhs.denominator_ref_;
        numerator_ref_ = rhs.numerator_ref_;
        description_ = rhs.description_;
      }
 
      virtual ~Ratio()
      {
      }
 
      Ratio& operator=(const Ratio& rhs)
      {
        if (&rhs != this)
        {
          ratio_value_ = rhs.ratio_value_;
          denominator_ref_ = rhs.denominator_ref_;
          numerator_ref_ = rhs.numerator_ref_;
          description_ = rhs.description_;
        }
        return *this;
      }
 
      // @TODO: members are public, names shouldn't end in underscores
      double ratio_value_;
      String denominator_ref_;
      String numerator_ref_;
      std::vector<String> description_;
      //TODO ratio cv info
    };
 
 
    ConsensusFeature();
 
    ConsensusFeature(const ConsensusFeature& rhs) = default;
 
    ConsensusFeature(ConsensusFeature&& rhs) = default;
 
    explicit ConsensusFeature(const BaseFeature& feature);
 
    ConsensusFeature(UInt64 map_index, const Peak2D& element, UInt64 element_index);
 
    ConsensusFeature(UInt64 map_index, const BaseFeature& element);
 
    ConsensusFeature& operator=(const ConsensusFeature& rhs) = default;
 
    ConsensusFeature& operator=(ConsensusFeature&& rhs) = default;
 
    ~ConsensusFeature() override;
 
 
 
 
    void insert(const ConsensusFeature& cf);
    void insert(ConsensusFeature&& cf);
 
    void insert(const FeatureHandle& handle);
    void insert(FeatureHandle&& handle);
 
    void insert(const HandleSetType& handle_set);
    void insert(HandleSetType&& handle_set);
 
    void insert(UInt64 map_index, const Peak2D& element, UInt64 element_index);
 
    void insert(UInt64 map_index, const BaseFeature& element);
 
    const HandleSetType& getFeatures() const;
 
    std::vector<FeatureHandle> getFeatureList() const;
 
    void setFeatures(HandleSetType h);
 
 
    DRange<2> getPositionRange() const;
    DRange<1> getIntensityRange() const;
 
 
    void computeConsensus();
 
    void computeMonoisotopicConsensus();
 
    void computeDechargeConsensus(const FeatureMap& fm, bool intensity_weighted_averaging = false);
 
    void addRatio(const Ratio& r);
 
    void setRatios(std::vector<Ratio>& rs);
 
    std::vector<Ratio> getRatios() const;
 
    std::vector<Ratio>& getRatios();
 
 
    Size size() const;
 
    const_iterator begin() const;
 
    iterator begin();
 
    const_iterator end() const;
 
    iterator end();
 
    const_reverse_iterator rbegin() const;
 
    reverse_iterator rbegin();
 
    const_reverse_iterator rend() const;
 
    reverse_iterator rend();
 
    void clear();
 
    bool empty() const;
 
private:
 
    HandleSetType handles_;
    std::vector<Ratio> ratios_;
 
 
  };
 
  OPENMS_DLLAPI std::ostream& operator<<(std::ostream& os, const ConsensusFeature& cons);
 
} // namespace OpenMS