IsotopeDistribution.h

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//                   OpenMS -- Open-Source Mass Spectrometry
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// Copyright The OpenMS Team -- Eberhard Karls University Tuebingen,
// ETH Zurich, and Freie Universitaet Berlin 2002-2023.
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// $Maintainer: Chris Bielow $
// $Authors: Clemens Groepl, Andreas Bertsch, Chris Bielow $
// --------------------------------------------------------------------------
 
#pragma once
 
#include <OpenMS/KERNEL/Peak1D.h>
#include <functional>
#include <vector>
 
namespace OpenMS
{
  class Element; 
 
  class OPENMS_DLLAPI IsotopeDistribution
  {
public:
 
 
    typedef Peak1D MassAbundance;
    typedef std::vector<MassAbundance> ContainerType;
    typedef ContainerType::iterator iterator;
    typedef ContainerType::iterator Iterator;
    typedef ContainerType::const_iterator const_iterator;
    typedef ContainerType::const_iterator ConstIterator;
 
    typedef ContainerType::reverse_iterator reverse_iterator;
    typedef ContainerType::reverse_iterator ReverseIterator;
    typedef ContainerType::const_reverse_iterator const_reverse_iterator;
    typedef ContainerType::const_reverse_iterator ConstReverseIterator;
 
    enum Sorted {INTENSITY, MASS, UNDEFINED};
 
 
 
    IsotopeDistribution();
 
    IsotopeDistribution(const IsotopeDistribution&) = default;
 
    IsotopeDistribution(IsotopeDistribution&&) noexcept = default;
 
    virtual ~IsotopeDistribution() = default;
 
 
 
    void set(const ContainerType & distribution);
 
    void set(ContainerType && distribution);
 
    const ContainerType & getContainer() const;
 
    Peak1D::CoordinateType getMax() const;
 
    Peak1D::CoordinateType getMin() const;
 
    Peak1D getMostAbundant() const;
 
    Size size() const;
 
    void clear();
 
    // resizes distribution container
    void resize(UInt size);
 
    void trimIntensities(double cutoff);
 
    void sortByIntensity();
 
    void sortByMass();
 
    void renormalize();
 
    void merge(double resolution, double min_prob);
 
    void trimRight(double cutoff);
 
    void trimLeft(double cutoff);
 
    double averageMass() const;
 
 
    IsotopeDistribution & operator=(const IsotopeDistribution & isotope_distribution);
 
    bool operator==(const IsotopeDistribution & isotope_distribution) const;
 
    bool operator!=(const IsotopeDistribution & isotope_distribution) const;
 
    bool operator<(const IsotopeDistribution & isotope_distribution) const;
 
 
    inline Iterator begin() { return distribution_.begin(); }
 
    inline Iterator end()   { return distribution_.end(); }
 
    inline ConstIterator begin() const { return distribution_.begin(); }
 
    inline ConstIterator end() const { return distribution_.end(); }
 
    inline ReverseIterator rbegin() { return distribution_.rbegin(); }
 
    inline ReverseIterator rend()   { return distribution_.rend(); }
 
    inline ConstReverseIterator rbegin() const { return distribution_.rbegin(); }
 
    inline ConstReverseIterator rend() const { return distribution_.rend(); }
 
    inline void insert(const Peak1D::CoordinateType& mass, const Peak1D::IntensityType& intensity)
    {
      distribution_.push_back(Peak1D(mass, intensity));
    }
 
 
    Peak1D& operator[](const Size& index){ return distribution_[index];}
    const Peak1D& operator[](const Size& index) const { return distribution_[index]; }
 
protected:   
 
    void sort_(std::function<bool(const MassAbundance& p1, const MassAbundance& p2)> sorter);
 
    void transform_(std::function<void(MassAbundance&)> lambda);
 
    ContainerType distribution_;
  };
 
 
} // namespace OpenMS