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 2002-2012.
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// $Maintainer: Erhan Kenar $
// $Authors: $
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#ifndef OPENMS_KERNEL_CONSENSUSFEATURE_H
#define OPENMS_KERNEL_CONSENSUSFEATURE_H

#include <OpenMS/DATASTRUCTURES/DRange.h>
#include <OpenMS/KERNEL/BaseFeature.h>
#include <OpenMS/KERNEL/FeatureHandle.h>
#include <OpenMS/KERNEL/FeatureMap.h>

#include <set>

namespace OpenMS
{
  class OPENMS_DLLAPI ConsensusFeature :
    public BaseFeature,
    public std::set<FeatureHandle, FeatureHandle::IndexLess>
  {
public:

    typedef std::set<FeatureHandle, FeatureHandle::IndexLess> HandleSetType;

    struct SizeLess :
      std::binary_function<ConsensusFeature, ConsensusFeature, bool>
    {
      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 :
      std::binary_function<ConsensusFeature, ConsensusFeature, bool>
    {
      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;
      }

      DoubleReal ratio_value_;
      String denominator_ref_;
      String numerator_ref_;
      std::vector<String> description_;
      //TODO ratio cv info
    };



    ConsensusFeature();

    ConsensusFeature(const ConsensusFeature & rhs);

    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);

    virtual ~ConsensusFeature();




    void insert(const FeatureHandle & handle);

    void insert(const 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;



    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();

private:
    std::vector<Ratio> ratios_;

  };

  OPENMS_DLLAPI std::ostream & operator<<(std::ostream & os, const ConsensusFeature & cons);

} // namespace OpenMS

#endif // OPENMS_KERNEL_CONSENSUSFEATURE_H